5VBF

Crystal structure of succinate semialdehyde dehydrogenase from Burkholderia vietnamiensis

PDB DOI: https://doi.org/10.2210/pdb5VBF/pdb

Classification: OXIDOREDUCTASE
Organism(s): Burkholderia vietnamiensis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-03-29 Released: 2017-04-12
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.196
R-Value Work: 0.147
R-Value Observed: 0.148

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of succinate semialdehyde dehydrogenase from Burkholderia vietnamiensis

Conrady, D.G., Fox III, D., Lorimer, D.D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 413.46 kDa
Atom Count: 31,891
Modelled Residue Count: 3,815
Deposited Residue Count: 3,824
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent succinate-semialdehyde dehydrogenase	A, B, C, D, E A, B, C, D, E, F, G, H	478	Burkholderia vietnamiensis	Mutation(s): 0 Gene Names: WK24_04400 EC: 1.2.1.16
UniProt
Find proteins for A4JQH6 (Burkholderia vietnamiensis (strain G4 / LMG 22486)) Explore A4JQH6 Go to UniProtKB: A4JQH6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A4JQH6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain DA [auth G] SDF format, chain GA [auth H] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain T [auth D] SDF format, chain W [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain DA [auth G] MOL2 format, chain GA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] MOL2 format, chain W [auth E] mmCIF format, chain AA [auth F] mmCIF format, chain DA [auth G] mmCIF format, chain GA [auth H] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain T [auth D] mmCIF format, chain W [auth E]	AA [auth F] DA [auth G] GA [auth H] I [auth A] M [auth B] AA [auth F], DA [auth G], GA [auth H], I [auth A], M [auth B], Q [auth C], T [auth D], W [auth E]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain DA [auth G] Focus chain GA [auth H] Focus chain I [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain T [auth D] Focus chain W [auth E] Interactions & Density Focus chain AA [auth F] Focus chain DA [auth G] Focus chain GA [auth H] Focus chain I [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain T [auth D] Focus chain W [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain EA [auth G] SDF format, chain HA [auth H] SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain U [auth D] SDF format, chain X [auth E] MOL2 format, chain BA [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain HA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain U [auth D] MOL2 format, chain X [auth E] mmCIF format, chain BA [auth F] mmCIF format, chain EA [auth G] mmCIF format, chain HA [auth H] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C] mmCIF format, chain U [auth D] mmCIF format, chain X [auth E]	BA [auth F] EA [auth G] HA [auth H] J [auth A] N [auth B] BA [auth F], EA [auth G], HA [auth H], J [auth A], N [auth B], R [auth C], U [auth D], X [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain J [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth E] Interactions & Density Focus chain BA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain J [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth E]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain IA [auth H] SDF format, chain K [auth A] SDF format, chain O [auth B] SDF format, chain Y [auth E] MOL2 format, chain IA [auth H] MOL2 format, chain K [auth A] MOL2 format, chain O [auth B] MOL2 format, chain Y [auth E] mmCIF format, chain IA [auth H] mmCIF format, chain K [auth A] mmCIF format, chain O [auth B] mmCIF format, chain Y [auth E]	IA [auth H], K [auth A], O [auth B], Y [auth E]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain IA [auth H] Focus chain K [auth A] Focus chain O [auth B] Focus chain Y [auth E] Interactions & Density Focus chain IA [auth H] Focus chain K [auth A] Focus chain O [auth B] Focus chain Y [auth E]
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain FA [auth G] SDF format, chain JA [auth H] SDF format, chain L [auth A] SDF format, chain P [auth B] SDF format, chain S [auth C] SDF format, chain V [auth D] SDF format, chain Z [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain FA [auth G] MOL2 format, chain JA [auth H] MOL2 format, chain L [auth A] MOL2 format, chain P [auth B] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D] MOL2 format, chain Z [auth E] mmCIF format, chain CA [auth F] mmCIF format, chain FA [auth G] mmCIF format, chain JA [auth H] mmCIF format, chain L [auth A] mmCIF format, chain P [auth B] mmCIF format, chain S [auth C] mmCIF format, chain V [auth D] mmCIF format, chain Z [auth E]	CA [auth F] FA [auth G] JA [auth H] L [auth A] P [auth B] CA [auth F], FA [auth G], JA [auth H], L [auth A], P [auth B], S [auth C], V [auth D], Z [auth E]	UNKNOWN ATOM OR ION X		Interactions Focus chain CA [auth F] Focus chain FA [auth G] Focus chain JA [auth H] Focus chain L [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain Z [auth E] Interactions & Density Focus chain CA [auth F] Focus chain FA [auth G] Focus chain JA [auth H] Focus chain L [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain Z [auth E]