7EXK | pdb_00007exk

An AA9 LPMO of Ceriporiopsis subvermispora

PDB DOI: https://doi.org/10.2210/pdb7EXK/pdb

Classification: OXIDOREDUCTASE
Organism(s): Gelatoporia subvermispora B
Expression System: Komagataella pastoris
Mutation(s): No

Deposited: 2021-05-27 Released: 2022-05-04
Deposition Author(s): Nguyen, H., Kondo, K., Nagata, T., Katahira, M., Mikami, B.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free:
0.230 (Depositor), 0.228 (DCC)
R-Value Work:
0.172 (Depositor)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Functional and Structural Characterizations of Lytic Polysaccharide Monooxygenase, Which Cooperates Synergistically with Cellulases, from Ceriporiopsis subvermispora.

Nguyen, H., Kondo, K., Yagi, Y., Iseki, Y., Okuoka, N., Watanabe, T., Mikami, B., Nagata, T., Katahira, M.

(2022) ACS Sustain Chem Eng 10: 923-934

DOI: https://doi.org/10.1021/acssuschemeng.1c06810

Macromolecule Content

Total Structure Weight: 144.38 kDa
Atom Count: 10,833
Modeled Residue Count: 1,302
Deposited Residue Count: 1,302
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoside hydrolase family 61 protein	A, B, C, D, E A, B, C, D, E, F	217	Gelatoporia subvermispora B	Mutation(s): 0 Gene Names: CERSUDRAFT_85414 EC: 1.14.99.56
UniProt
Find proteins for M2RAI8 (Ceriporiopsis subvermispora (strain B)) Explore M2RAI8 Go to UniProtKB: M2RAI8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	M2RAI8
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D Focus chain E Focus chain F
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain ZB [auth F] SDF format, chain U [auth B] SDF format, chain SA [auth C] SDF format, chain NB [auth E] SDF format, chain G [auth A] SDF format, chain AB [auth D] MOL2 format, chain ZB [auth F] MOL2 format, chain U [auth B] MOL2 format, chain SA [auth C] MOL2 format, chain NB [auth E] MOL2 format, chain G [auth A] MOL2 format, chain AB [auth D] mmCIF format, chain ZB [auth F] mmCIF format, chain U [auth B] mmCIF format, chain SA [auth C] mmCIF format, chain NB [auth E] mmCIF format, chain G [auth A] mmCIF format, chain AB [auth D]	AB [auth D] G [auth A] NB [auth E] SA [auth C] U [auth B] AB [auth D], G [auth A], NB [auth E], SA [auth C], U [auth B], ZB [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth D] Focus chain G [auth A] Focus chain NB [auth E] Focus chain SA [auth C] Focus chain U [auth B] Focus chain ZB [auth F] Interactions & Density Focus chain AB [auth D] Focus chain G [auth A] Focus chain NB [auth E] Focus chain SA [auth C] Focus chain U [auth B] Focus chain ZB [auth F]
XYS Query on XYS Download:Ideal Coordinates CCD File SDF format, chain RA [auth B] MOL2 format, chain RA [auth B] mmCIF format, chain RA [auth B]	RA [auth B]	alpha-D-xylopyranose C₅ H₁₀ O₅ SRBFZHDQGSBBOR-LECHCGJUSA-N		Interactions Focus chain RA [auth B] Interactions & Density Focus chain RA [auth B]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain UA [auth C] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain BC [auth F] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain UA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain BC [auth F] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain UA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain BC [auth F]	BC [auth F] I [auth A] J [auth A] UA [auth C] W [auth B] BC [auth F], I [auth A], J [auth A], UA [auth C], W [auth B], X [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain BC [auth F] Focus chain I [auth A] Focus chain J [auth A] Focus chain UA [auth C] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain BC [auth F] Focus chain I [auth A] Focus chain J [auth A] Focus chain UA [auth C] Focus chain W [auth B] Focus chain X [auth B]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain TA [auth C] SDF format, chain OB [auth E] SDF format, chain H [auth A] SDF format, chain BB [auth D] SDF format, chain AC [auth F] MOL2 format, chain V [auth B] MOL2 format, chain TA [auth C] MOL2 format, chain OB [auth E] MOL2 format, chain H [auth A] MOL2 format, chain BB [auth D] MOL2 format, chain AC [auth F] mmCIF format, chain V [auth B] mmCIF format, chain TA [auth C] mmCIF format, chain OB [auth E] mmCIF format, chain H [auth A] mmCIF format, chain BB [auth D] mmCIF format, chain AC [auth F]	AC [auth F] BB [auth D] H [auth A] OB [auth E] TA [auth C] AC [auth F], BB [auth D], H [auth A], OB [auth E], TA [auth C], V [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain AC [auth F] Focus chain BB [auth D] Focus chain H [auth A] Focus chain OB [auth E] Focus chain TA [auth C] Focus chain V [auth B] Interactions & Density Focus chain AC [auth F] Focus chain BB [auth D] Focus chain H [auth A] Focus chain OB [auth E] Focus chain TA [auth C] Focus chain V [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain ZA [auth C] SDF format, chain Z [auth B] SDF format, chain YB [auth E] SDF format, chain YA [auth C] SDF format, chain Y [auth B] SDF format, chain XB [auth E] SDF format, chain XA [auth C] SDF format, chain WB [auth E] SDF format, chain WA [auth C] SDF format, chain VB [auth E] SDF format, chain VA [auth C] SDF format, chain UB [auth E] SDF format, chain TB [auth E] SDF format, chain T [auth A] SDF format, chain SB [auth E] SDF format, chain S [auth A] SDF format, chain RB [auth E] SDF format, chain R [auth A] SDF format, chain QB [auth E] SDF format, chain QA [auth B] SDF format, chain Q [auth A] SDF format, chain PB [auth E] SDF format, chain PA [auth B] SDF format, chain P [auth A] SDF format, chain OA [auth B] SDF format, chain O [auth A] SDF format, chain NC [auth F] SDF format, chain NA [auth B] SDF format, chain N [auth A] SDF format, chain MC [auth F] SDF format, chain MA [auth B] SDF format, chain M [auth A] SDF format, chain LC [auth F] SDF format, chain LB [auth D] SDF format, chain LA [auth B] SDF format, chain L [auth A] SDF format, chain KC [auth F] SDF format, chain KB [auth D] SDF format, chain KA [auth B] SDF format, chain K [auth A] SDF format, chain JC [auth F] SDF format, chain JB [auth D] SDF format, chain JA [auth B] SDF format, chain IC [auth F] SDF format, chain IB [auth D] SDF format, chain IA [auth B] SDF format, chain HC [auth F] SDF format, chain HB [auth D] SDF format, chain HA [auth B] SDF format, chain GC [auth F] SDF format, chain GB [auth D] SDF format, chain GA [auth B] SDF format, chain FC [auth F] SDF format, chain FB [auth D] SDF format, chain FA [auth B] SDF format, chain EC [auth F] SDF format, chain EB [auth D] SDF format, chain EA [auth B] SDF format, chain DC [auth F] SDF format, chain DB [auth D] SDF format, chain DA [auth B] SDF format, chain CC [auth F] SDF format, chain CB [auth D] SDF format, chain CA [auth B] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain ZA [auth C] MOL2 format, chain Z [auth B] MOL2 format, chain YB [auth E] MOL2 format, chain YA [auth C] MOL2 format, chain Y [auth B] MOL2 format, chain XB [auth E] MOL2 format, chain XA [auth C] MOL2 format, chain WB [auth E] MOL2 format, chain WA [auth C] MOL2 format, chain VB [auth E] MOL2 format, chain VA [auth C] MOL2 format, chain UB [auth E] MOL2 format, chain TB [auth E] MOL2 format, chain T [auth A] MOL2 format, chain SB [auth E] MOL2 format, chain S [auth A] MOL2 format, chain RB [auth E] MOL2 format, chain R [auth A] MOL2 format, chain QB [auth E] MOL2 format, chain QA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain PB [auth E] MOL2 format, chain PA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain NC [auth F] MOL2 format, chain NA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain MC [auth F] MOL2 format, chain MA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain LC [auth F] MOL2 format, chain LB [auth D] MOL2 format, chain LA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain KC [auth F] MOL2 format, chain KB [auth D] MOL2 format, chain KA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain JC [auth F] MOL2 format, chain JB [auth D] MOL2 format, chain JA [auth B] MOL2 format, chain IC [auth F] MOL2 format, chain IB [auth D] MOL2 format, chain IA [auth B] MOL2 format, chain HC [auth F] MOL2 format, chain HB [auth D] MOL2 format, chain HA [auth B] MOL2 format, chain GC [auth F] MOL2 format, chain GB [auth D] MOL2 format, chain GA [auth B] MOL2 format, chain FC [auth F] MOL2 format, chain FB [auth D] MOL2 format, chain FA [auth B] MOL2 format, chain EC [auth F] MOL2 format, chain EB [auth D] MOL2 format, chain EA [auth B] MOL2 format, chain DC [auth F] MOL2 format, chain DB [auth D] MOL2 format, chain DA [auth B] MOL2 format, chain CC [auth F] MOL2 format, chain CB [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain ZA [auth C] mmCIF format, chain Z [auth B] mmCIF format, chain YB [auth E] mmCIF format, chain YA [auth C] mmCIF format, chain Y [auth B] mmCIF format, chain XB [auth E] mmCIF format, chain XA [auth C] mmCIF format, chain WB [auth E] mmCIF format, chain WA [auth C] mmCIF format, chain VB [auth E] mmCIF format, chain VA [auth C] mmCIF format, chain UB [auth E] mmCIF format, chain TB [auth E] mmCIF format, chain T [auth A] mmCIF format, chain SB [auth E] mmCIF format, chain S [auth A] mmCIF format, chain RB [auth E] mmCIF format, chain R [auth A] mmCIF format, chain QB [auth E] mmCIF format, chain QA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain PB [auth E] mmCIF format, chain PA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain NC [auth F] mmCIF format, chain NA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain MC [auth F] mmCIF format, chain MA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain LC [auth F] mmCIF format, chain LB [auth D] mmCIF format, chain LA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain KC [auth F] mmCIF format, chain KB [auth D] mmCIF format, chain KA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain JC [auth F] mmCIF format, chain JB [auth D] mmCIF format, chain JA [auth B] mmCIF format, chain IC [auth F] mmCIF format, chain IB [auth D] mmCIF format, chain IA [auth B] mmCIF format, chain HC [auth F] mmCIF format, chain HB [auth D] mmCIF format, chain HA [auth B] mmCIF format, chain GC [auth F] mmCIF format, chain GB [auth D] mmCIF format, chain GA [auth B] mmCIF format, chain FC [auth F] mmCIF format, chain FB [auth D] mmCIF format, chain FA [auth B] mmCIF format, chain EC [auth F] mmCIF format, chain EB [auth D] mmCIF format, chain EA [auth B] mmCIF format, chain DC [auth F] mmCIF format, chain DB [auth D] mmCIF format, chain DA [auth B] mmCIF format, chain CC [auth F] mmCIF format, chain CB [auth D] mmCIF format, chain CA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] CA [auth B] CB [auth D] CC [auth F] AA [auth B], BA [auth B], CA [auth B], CB [auth D], CC [auth F], DA [auth B], DB [auth D], DC [auth F], EA [auth B], EB [auth D], EC [auth F], FA [auth B], FB [auth D], FC [auth F], GA [auth B], GB [auth D], GC [auth F], HA [auth B], HB [auth D], HC [auth F], IA [auth B], IB [auth D], IC [auth F], JA [auth B], JB [auth D], JC [auth F], K [auth A], KA [auth B], KB [auth D], KC [auth F], L [auth A], LA [auth B], LB [auth D], LC [auth F], M [auth A], MA [auth B], MC [auth F], N [auth A], NA [auth B], NC [auth F], O [auth A], OA [auth B], P [auth A], PA [auth B], PB [auth E], Q [auth A], QA [auth B], QB [auth E], R [auth A], RB [auth E], S [auth A], SB [auth E], T [auth A], TB [auth E], UB [auth E], VA [auth C], VB [auth E], WA [auth C], WB [auth E], XA [auth C], XB [auth E], Y [auth B], YA [auth C], YB [auth E], Z [auth B], ZA [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain CC [auth F] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain DC [auth F] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain EC [auth F] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain FC [auth F] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain GC [auth F] Focus chain HA [auth B] Focus chain HB [auth D] Focus chain HC [auth F] Focus chain IA [auth B] Focus chain IB [auth D] Focus chain IC [auth F] Focus chain JA [auth B] Focus chain JB [auth D] Focus chain JC [auth F] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth D] Focus chain KC [auth F] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth D] Focus chain LC [auth F] Focus chain M [auth A] Focus chain MA [auth B] Focus chain MC [auth F] Focus chain N [auth A] Focus chain NA [auth B] Focus chain NC [auth F] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain PB [auth E] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain QB [auth E] Focus chain R [auth A] Focus chain RB [auth E] Focus chain S [auth A] Focus chain SB [auth E] Focus chain T [auth A] Focus chain TB [auth E] Focus chain UB [auth E] Focus chain VA [auth C] Focus chain VB [auth E] Focus chain WA [auth C] Focus chain WB [auth E] Focus chain XA [auth C] Focus chain XB [auth E] Focus chain Y [auth B] Focus chain YA [auth C] Focus chain YB [auth E] Focus chain Z [auth B] Focus chain ZA [auth C] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain CC [auth F] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain DC [auth F] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain EC [auth F] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain FC [auth F] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain GC [auth F] Focus chain HA [auth B] Focus chain HB [auth D] Focus chain HC [auth F] Focus chain IA [auth B] Focus chain IB [auth D] Focus chain IC [auth F] Focus chain JA [auth B] Focus chain JB [auth D] Focus chain JC [auth F] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth D] Focus chain KC [auth F] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth D] Focus chain LC [auth F] Focus chain M [auth A] Focus chain MA [auth B] Focus chain MC [auth F] Focus chain N [auth A] Focus chain NA [auth B] Focus chain NC [auth F] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain PB [auth E] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain QB [auth E] Focus chain R [auth A] Focus chain RB [auth E] Focus chain S [auth A] Focus chain SB [auth E] Focus chain T [auth A] Focus chain TB [auth E] Focus chain UB [auth E] Focus chain VA [auth C] Focus chain VB [auth E] Focus chain WA [auth C] Focus chain WB [auth E] Focus chain XA [auth C] Focus chain XB [auth E] Focus chain Y [auth B] Focus chain YA [auth C] Focus chain YB [auth E] Focus chain Z [auth B] Focus chain ZA [auth C]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain OC [auth F] SDF format, chain MB [auth D] MOL2 format, chain OC [auth F] MOL2 format, chain MB [auth D] mmCIF format, chain OC [auth F] mmCIF format, chain MB [auth D]	MB [auth D], OC [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain MB [auth D] Focus chain OC [auth F] Interactions & Density Focus chain MB [auth D] Focus chain OC [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free: 0.230 (Depositor), 0.228 (DCC)
R-Value Work: 0.172 (Depositor)
R-Value Observed: 0.175 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.063	α = 90
b = 52.428	β = 90.553
c = 134.625	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-05-04

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	20H03192
Japan Society for the Promotion of Science (JSPS)	Japan	20K21477
Japan Society for the Promotion of Science (JSPS)	Japan	20K06524