8U2M | pdb_00008u2m

Structure of P450Blt from Micromonospora sp. MW-13 in Complex with Biarylitide

PDB DOI: https://doi.org/10.2210/pdb8U2M/pdb

Classification: OXIDOREDUCTASE
Organism(s): Micromonospora sp. MW-13, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-09-06 Released: 2024-01-10
Deposition Author(s): Hansen, M.H., Cryle, M.J.
Funding Organization(s): Australian Research Council (ARC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free:
0.229 (Depositor), 0.229 (DCC)
R-Value Work:
0.199 (Depositor), 0.199 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structural Insights into a Side Chain Cross-Linking Biarylitide P450 from RiPP Biosynthesis

Hansen, M.H., Keto, A., Treisman, M., Sasi, V.M., Coe, L., Zhao, Y., Padva, L., Hess, C., Leichthammer, V., Machell, D.L., Schittenhelm, R.B., Jackson, C.J., Tailhades, J., Crusemann, M., De Voss, J.J., Krenske, E.H., Cryle, M.J.

(2024) ACS Catal : 812-826

DOI: https://doi.org/10.1021/acscatal.3c05417

Macromolecule Content

Total Structure Weight: 139.97 kDa
Atom Count: 9,655
Modeled Residue Count: 1,149
Deposited Residue Count: 1,265
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450-SU1	A, B, C	420	Micromonospora sp. MW-13	Mutation(s): 0 Gene Names: C5N14_21030 EC: 1.14
UniProt
Find proteins for A0ACD6BAH8 (Micromonospora sp. MW-13) Explore A0ACD6BAH8 Go to UniProtKB: A0ACD6BAH8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6BAH8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MET-ARG-TYR-LEU-HIS	D	5	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain Q [auth B] SDF format, chain V [auth C] MOL2 format, chain J [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain V [auth C] mmCIF format, chain J [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain V [auth C]	J [auth A], Q [auth B], V [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain J [auth A] Focus chain Q [auth B] Focus chain V [auth C] Interactions & Density Focus chain J [auth A] Focus chain Q [auth B] Focus chain V [auth C]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
TOE Query on TOE Download:Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B] mmCIF format, chain O [auth B]	O [auth B]	2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL C₇ H₁₆ O₄ JLGLQAWTXXGVEM-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]
MRY Query on MRY Download:Ideal Coordinates CCD File SDF format, chain P [auth B] MOL2 format, chain P [auth B] mmCIF format, chain P [auth B]	P [auth B]	MESO-ERYTHRITOL C₄ H₁₀ O₄ UNXHWFMMPAWVPI-ZXZARUISSA-N		Interactions Focus chain P [auth B] Interactions & Density Focus chain P [auth B]
TFA Query on TFA Download:Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain W [auth C] SDF format, chain X [auth C] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C]	S [auth B], T [auth B], W [auth C], X [auth C]	trifluoroacetic acid C₂ H F₃ O₂ DTQVDTLACAAQTR-UHFFFAOYSA-N		Interactions Focus chain S [auth B] Focus chain T [auth B] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain S [auth B] Focus chain T [auth B] Focus chain W [auth C] Focus chain X [auth C]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain R [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain R [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain N [auth B] mmCIF format, chain R [auth B]	E [auth A] F [auth A] H [auth A] I [auth A] N [auth B] E [auth A], F [auth A], H [auth A], I [auth A], N [auth B], R [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain R [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain R [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain U [auth B] SDF format, chain Y [auth C] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain U [auth B] MOL2 format, chain Y [auth C] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain U [auth B] mmCIF format, chain Y [auth C]	K [auth A], L [auth A], M [auth A], U [auth B], Y [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain U [auth B] Focus chain Y [auth C] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain U [auth B] Focus chain Y [auth C]