3OZM

Crystal structure of enolase superfamily member from Bordetella bronchiseptica complexed with Mg, m-Xylarate and L-Lyxarate

PDB DOI: https://doi.org/10.2210/pdb3OZM/pdb

Classification: TRANSFERASE
Organism(s): Bordetella bronchiseptica
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-09-25 Released: 2011-09-28
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Wichelecki, D., Gerlt, J.A., Almo, S.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.222
R-Value Work: 0.191
R-Value Observed: 0.193

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of enolase superfamily member from Bordetella bronchiseptica complexed with Mg, m-Xylarate and L-Lyxarate

Fedorov, A.A., Fedorov, E.V., Wichelecki, D., Gerlt, J.A., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 342.12 kDa
Atom Count: 26,586
Modelled Residue Count: 3,077
Deposited Residue Count: 3,112
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative mandelate racemase	A, B, C, D, E A, B, C, D, E, F, G, H	389	Bordetella bronchiseptica	Mutation(s): 0 Gene Names: BB4687
UniProt
Find proteins for A0A0H3LT39 (Bordetella bronchiseptica (strain ATCC BAA-588 / NCTC 13252 / RB50)) Explore A0A0H3LT39 Go to UniProtKB: A0A0H3LT39
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H3LT39
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LY9 Query on LY9 Download Ideal Coordinates CCD File SDF format, chain GA [auth H] SDF format, chain V [auth D] MOL2 format, chain GA [auth H] MOL2 format, chain V [auth D]	GA [auth H], V [auth D]	L-arabinaric acid C₅ H₈ O₇ NPTTZSYLTYJCPR-PWNYCUMCSA-N		Interactions Focus chain GA [auth H] Focus chain V [auth D] Interactions & Density Focus chain GA [auth H] Focus chain V [auth D]
DXL Query on DXL Download Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain DA [auth G] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain Y [auth E] MOL2 format, chain BA [auth F] MOL2 format, chain DA [auth G] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain Y [auth E]	BA [auth F] DA [auth G] J [auth A] M [auth B] Q [auth C] BA [auth F], DA [auth G], J [auth A], M [auth B], Q [auth C], Y [auth E]	D-xylaric acid C₅ H₈ O₇ NPTTZSYLTYJCPR-FFEAPLRNSA-N		Interactions Focus chain BA [auth F] Focus chain DA [auth G] Focus chain J [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain Y [auth E] Interactions & Density Focus chain BA [auth F] Focus chain DA [auth G] Focus chain J [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain Y [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain EA [auth G] SDF format, chain HA [auth H] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain W [auth D] SDF format, chain Z [auth E] MOL2 format, chain EA [auth G] MOL2 format, chain HA [auth H] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain W [auth D] MOL2 format, chain Z [auth E]	EA [auth G] HA [auth H] K [auth A] N [auth B] O [auth B] EA [auth G], HA [auth H], K [auth A], N [auth B], O [auth B], R [auth C], S [auth C], T [auth C], W [auth D], Z [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain EA [auth G] Focus chain HA [auth H] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain W [auth D] Focus chain Z [auth E] Interactions & Density Focus chain EA [auth G] Focus chain HA [auth H] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain W [auth D] Focus chain Z [auth E]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain CA [auth G] SDF format, chain FA [auth H] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain U [auth D] SDF format, chain X [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain CA [auth G] MOL2 format, chain FA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain U [auth D] MOL2 format, chain X [auth E]	AA [auth F] CA [auth G] FA [auth H] I [auth A] L [auth B] AA [auth F], CA [auth G], FA [auth H], I [auth A], L [auth B], P [auth C], U [auth D], X [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain CA [auth G] Focus chain FA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain U [auth D] Focus chain X [auth E] Interactions & Density Focus chain AA [auth F] Focus chain CA [auth G] Focus chain FA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain U [auth D] Focus chain X [auth E]