8F9X

Cyclase-PTE

PDB DOI: https://doi.org/10.2210/pdb8F9X/pdb

Classification: HYDROLASE
Organism(s): Ruegeria pomeroyi DSS-3
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-11-24 Released: 2023-12-06
Deposition Author(s): Ji, D., Frkic, R.L., Jackson, C.J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free: 0.251
R-Value Work: 0.203
R-Value Observed: 0.208

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Cyclase-PTE

Ji, D., Frkic, R.L., Jackson, C.J.

To be published.

Macromolecule Content

Total Structure Weight: 249.66 kDa
Atom Count: 17,461
Modelled Residue Count: 2,275
Deposited Residue Count: 2,300
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclase family protein	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	230	Ruegeria pomeroyi DSS-3	Mutation(s): 0 Gene Names: SPO0761
UniProt
Find proteins for Q5LVE1 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3)) Explore Q5LVE1 Go to UniProtKB: Q5LVE1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5LVE1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BTB Query on BTB Download Ideal Coordinates CCD File SDF format, chain AC [auth J] SDF format, chain CB [auth G] SDF format, chain DB [auth G] SDF format, chain IA [auth D] SDF format, chain KB [auth H] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain RB [auth I] SDF format, chain UA [auth F] SDF format, chain UB [auth I] SDF format, chain V [auth B] SDF format, chain VA [auth F] SDF format, chain Z [auth C] SDF format, chain ZB [auth J] MOL2 format, chain AC [auth J] MOL2 format, chain CB [auth G] MOL2 format, chain DB [auth G] MOL2 format, chain IA [auth D] MOL2 format, chain KB [auth H] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain RB [auth I] MOL2 format, chain UA [auth F] MOL2 format, chain UB [auth I] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth F] MOL2 format, chain Z [auth C] MOL2 format, chain ZB [auth J] mmCIF format, chain AC [auth J] mmCIF format, chain CB [auth G] mmCIF format, chain DB [auth G] mmCIF format, chain IA [auth D] mmCIF format, chain KB [auth H] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain RB [auth I] mmCIF format, chain UA [auth F] mmCIF format, chain UB [auth I] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth F] mmCIF format, chain Z [auth C] mmCIF format, chain ZB [auth J]	AC [auth J] CB [auth G] DB [auth G] IA [auth D] KB [auth H] AC [auth J], CB [auth G], DB [auth G], IA [auth D], KB [auth H], N [auth A], O [auth A], RB [auth I], UA [auth F], UB [auth I], V [auth B], VA [auth F], Z [auth C], ZB [auth J]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain AC [auth J] Focus chain CB [auth G] Focus chain DB [auth G] Focus chain IA [auth D] Focus chain KB [auth H] Focus chain N [auth A] Focus chain O [auth A] Focus chain RB [auth I] Focus chain UA [auth F] Focus chain UB [auth I] Focus chain V [auth B] Focus chain VA [auth F] Focus chain Z [auth C] Focus chain ZB [auth J] Interactions & Density Focus chain AC [auth J] Focus chain CB [auth G] Focus chain DB [auth G] Focus chain IA [auth D] Focus chain KB [auth H] Focus chain N [auth A] Focus chain O [auth A] Focus chain RB [auth I] Focus chain UA [auth F] Focus chain UB [auth I] Focus chain V [auth B] Focus chain VA [auth F] Focus chain Z [auth C] Focus chain ZB [auth J]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain DA [auth C] MOL2 format, chain DA [auth C] mmCIF format, chain DA [auth C]	DA [auth C]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain DA [auth C] Interactions & Density Focus chain DA [auth C]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain HA [auth D] SDF format, chain JB [auth H] SDF format, chain NA [auth E] SDF format, chain QB [auth I] SDF format, chain U [auth B] SDF format, chain YB [auth J] MOL2 format, chain HA [auth D] MOL2 format, chain JB [auth H] MOL2 format, chain NA [auth E] MOL2 format, chain QB [auth I] MOL2 format, chain U [auth B] MOL2 format, chain YB [auth J] mmCIF format, chain HA [auth D] mmCIF format, chain JB [auth H] mmCIF format, chain NA [auth E] mmCIF format, chain QB [auth I] mmCIF format, chain U [auth B] mmCIF format, chain YB [auth J]	HA [auth D] JB [auth H] NA [auth E] QB [auth I] U [auth B] HA [auth D], JB [auth H], NA [auth E], QB [auth I], U [auth B], YB [auth J]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain HA [auth D] Focus chain JB [auth H] Focus chain NA [auth E] Focus chain QB [auth I] Focus chain U [auth B] Focus chain YB [auth J] Interactions & Density Focus chain HA [auth D] Focus chain JB [auth H] Focus chain NA [auth E] Focus chain QB [auth I] Focus chain U [auth B] Focus chain YB [auth J]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain AB [auth G] SDF format, chain BB [auth G] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain GB [auth H] SDF format, chain HB [auth H] SDF format, chain IB [auth H] SDF format, chain K [auth A] SDF format, chain KA [auth E] SDF format, chain L [auth A] SDF format, chain LA [auth E] SDF format, chain M [auth A] SDF format, chain MA [auth E] SDF format, chain NB [auth I] SDF format, chain OB [auth I] SDF format, chain PB [auth I] SDF format, chain R [auth B] SDF format, chain RA [auth F] SDF format, chain S [auth B] SDF format, chain SA [auth F] SDF format, chain T [auth B] SDF format, chain TA [auth F] SDF format, chain VB [auth J] SDF format, chain W [auth C] SDF format, chain WB [auth J] SDF format, chain X [auth C] SDF format, chain XB [auth J] SDF format, chain Y [auth C] SDF format, chain ZA [auth G] MOL2 format, chain AB [auth G] MOL2 format, chain BB [auth G] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain GB [auth H] MOL2 format, chain HB [auth H] MOL2 format, chain IB [auth H] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth E] MOL2 format, chain NB [auth I] MOL2 format, chain OB [auth I] MOL2 format, chain PB [auth I] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth F] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth F] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth F] MOL2 format, chain VB [auth J] MOL2 format, chain W [auth C] MOL2 format, chain WB [auth J] MOL2 format, chain X [auth C] MOL2 format, chain XB [auth J] MOL2 format, chain Y [auth C] MOL2 format, chain ZA [auth G] mmCIF format, chain AB [auth G] mmCIF format, chain BB [auth G] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain GB [auth H] mmCIF format, chain HB [auth H] mmCIF format, chain IB [auth H] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth E] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth E] mmCIF format, chain NB [auth I] mmCIF format, chain OB [auth I] mmCIF format, chain PB [auth I] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth F] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth F] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth F] mmCIF format, chain VB [auth J] mmCIF format, chain W [auth C] mmCIF format, chain WB [auth J] mmCIF format, chain X [auth C] mmCIF format, chain XB [auth J] mmCIF format, chain Y [auth C] mmCIF format, chain ZA [auth G]	AB [auth G] BB [auth G] EA [auth D] FA [auth D] GA [auth D] AB [auth G], BB [auth G], EA [auth D], FA [auth D], GA [auth D], GB [auth H], HB [auth H], IB [auth H], K [auth A], KA [auth E], L [auth A], LA [auth E], M [auth A], MA [auth E], NB [auth I], OB [auth I], PB [auth I], R [auth B], RA [auth F], S [auth B], SA [auth F], T [auth B], TA [auth F], VB [auth J], W [auth C], WB [auth J], X [auth C], XB [auth J], Y [auth C], ZA [auth G]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AB [auth G] Focus chain BB [auth G] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain GB [auth H] Focus chain HB [auth H] Focus chain IB [auth H] Focus chain K [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain M [auth A] Focus chain MA [auth E] Focus chain NB [auth I] Focus chain OB [auth I] Focus chain PB [auth I] Focus chain R [auth B] Focus chain RA [auth F] Focus chain S [auth B] Focus chain SA [auth F] Focus chain T [auth B] Focus chain TA [auth F] Focus chain VB [auth J] Focus chain W [auth C] Focus chain WB [auth J] Focus chain X [auth C] Focus chain XB [auth J] Focus chain Y [auth C] Focus chain ZA [auth G] Interactions & Density Focus chain AB [auth G] Focus chain BB [auth G] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain GB [auth H] Focus chain HB [auth H] Focus chain IB [auth H] Focus chain K [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain M [auth A] Focus chain MA [auth E] Focus chain NB [auth I] Focus chain OB [auth I] Focus chain PB [auth I] Focus chain R [auth B] Focus chain RA [auth F] Focus chain S [auth B] Focus chain SA [auth F] Focus chain T [auth B] Focus chain TA [auth F] Focus chain VB [auth J] Focus chain W [auth C] Focus chain WB [auth J] Focus chain X [auth C] Focus chain XB [auth J] Focus chain Y [auth C] Focus chain ZA [auth G]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain BC [auth J] SDF format, chain CA [auth C] SDF format, chain EB [auth G] SDF format, chain FB [auth G] SDF format, chain JA [auth D] SDF format, chain LB [auth H] SDF format, chain MB [auth H] SDF format, chain OA [auth E] SDF format, chain P [auth A] SDF format, chain PA [auth E] SDF format, chain Q [auth A] SDF format, chain QA [auth E] SDF format, chain SB [auth I] SDF format, chain TB [auth I] SDF format, chain WA [auth F] SDF format, chain XA [auth F] SDF format, chain YA [auth F] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain BC [auth J] MOL2 format, chain CA [auth C] MOL2 format, chain EB [auth G] MOL2 format, chain FB [auth G] MOL2 format, chain JA [auth D] MOL2 format, chain LB [auth H] MOL2 format, chain MB [auth H] MOL2 format, chain OA [auth E] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth E] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth E] MOL2 format, chain SB [auth I] MOL2 format, chain TB [auth I] MOL2 format, chain WA [auth F] MOL2 format, chain XA [auth F] MOL2 format, chain YA [auth F] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain BC [auth J] mmCIF format, chain CA [auth C] mmCIF format, chain EB [auth G] mmCIF format, chain FB [auth G] mmCIF format, chain JA [auth D] mmCIF format, chain LB [auth H] mmCIF format, chain MB [auth H] mmCIF format, chain OA [auth E] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth E] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth E] mmCIF format, chain SB [auth I] mmCIF format, chain TB [auth I] mmCIF format, chain WA [auth F] mmCIF format, chain XA [auth F] mmCIF format, chain YA [auth F]	AA [auth C] BA [auth C] BC [auth J] CA [auth C] EB [auth G] AA [auth C], BA [auth C], BC [auth J], CA [auth C], EB [auth G], FB [auth G], JA [auth D], LB [auth H], MB [auth H], OA [auth E], P [auth A], PA [auth E], Q [auth A], QA [auth E], SB [auth I], TB [auth I], WA [auth F], XA [auth F], YA [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain BC [auth J] Focus chain CA [auth C] Focus chain EB [auth G] Focus chain FB [auth G] Focus chain JA [auth D] Focus chain LB [auth H] Focus chain MB [auth H] Focus chain OA [auth E] Focus chain P [auth A] Focus chain PA [auth E] Focus chain Q [auth A] Focus chain QA [auth E] Focus chain SB [auth I] Focus chain TB [auth I] Focus chain WA [auth F] Focus chain XA [auth F] Focus chain YA [auth F] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain BC [auth J] Focus chain CA [auth C] Focus chain EB [auth G] Focus chain FB [auth G] Focus chain JA [auth D] Focus chain LB [auth H] Focus chain MB [auth H] Focus chain OA [auth E] Focus chain P [auth A] Focus chain PA [auth E] Focus chain Q [auth A] Focus chain QA [auth E] Focus chain SB [auth I] Focus chain TB [auth I] Focus chain WA [auth F] Focus chain XA [auth F] Focus chain YA [auth F]