6KMA

Crystal structure of SucA with glycolaldehyde-1-13C from Vibrio vulnificus

PDB DOI: https://doi.org/10.2210/pdb6KMA/pdb

Classification: OXIDOREDUCTASE
Organism(s): Vibrio vulnificus CMCP6
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-07-31 Released: 2020-08-05
Deposition Author(s): Seo, P.W., Kim, J.S.
Funding Organization(s): National Research Foundation (Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free: 0.230
R-Value Work: 0.200
R-Value Observed: 0.201

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Understanding the molecular properties of the E1 subunit (SucA) of alpha-ketoglutarate dehydrogenase complex from Vibrio vulnificus for the enantioselective ligation of acetaldehydes into (R)-acetoin.

Seo, P.W., Jo, H.J., Hwang, I.Y., Jeong, H.Y., Kim, J.H., Kim, J.W., Lee, E.Y., Park, J.B., Kim, J.S.

(2020) Catal Sci Technol

DOI: https://doi.org/10.1039/C9CY01566C

Macromolecule Content

Total Structure Weight: 401.55 kDa
Atom Count: 27,925
Modelled Residue Count: 3,351
Deposited Residue Count: 3,544
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxoglutarate dehydrogenase (Succinyl-transferring), E1 component	A, B, C, D	886	Vibrio vulnificus CMCP6	Mutation(s): 0 Gene Names: sucA, VV1_0157 EC: 1.2.4.2
UniProt
Find proteins for A0A3Q0L1E1 (Vibrio vulnificus (strain CMCP6)) Explore A0A3Q0L1E1 Go to UniProtKB: A0A3Q0L1E1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A3Q0L1E1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TPP (Subject of Investigation/LOI) Query on TPP Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain N [auth B] SDF format, chain S [auth C] SDF format, chain Y [auth D] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain S [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain S [auth C] mmCIF format, chain Y [auth D]	H [auth A], N [auth B], S [auth C], Y [auth D]	THIAMINE DIPHOSPHATE C₁₂ H₁₉ N₄ O₇ P₂ S AYEKOFBPNLCAJY-UHFFFAOYSA-O		Interactions Focus chain H [auth A] Focus chain N [auth B] Focus chain S [auth C] Focus chain Y [auth D]
P6G Query on P6G Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain W [auth D] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain W [auth D] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain P [auth C] mmCIF format, chain W [auth D]	E [auth A], L [auth B], P [auth C], W [auth D]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain W [auth D]
DW3 (Subject of Investigation/LOI) Query on DW3 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth B] SDF format, chain O [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain Z [auth D] SDF format, chain V [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth B] MOL2 format, chain O [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain V [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth B] mmCIF format, chain O [auth B] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain Z [auth D] mmCIF format, chain V [auth D]	I [auth A] J [auth A] K [auth B] O [auth B] T [auth C] I [auth A], J [auth A], K [auth B], O [auth B], T [auth C], U [auth C], V [auth D], Z [auth D]	2-oxidanylethanal C₂ H₄ O₂ WGCNASOHLSPBMP-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain O [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth D] Focus chain Z [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain Q [auth C] MOL2 format, chain F [auth A] MOL2 format, chain Q [auth C] mmCIF format, chain F [auth A] mmCIF format, chain Q [auth C]	F [auth A], Q [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain Q [auth C]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth B] SDF format, chain R [auth C] SDF format, chain X [auth D] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] MOL2 format, chain X [auth D] mmCIF format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain R [auth C] mmCIF format, chain X [auth D]	G [auth A], M [auth B], R [auth C], X [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain X [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free: 0.230
R-Value Work: 0.200
R-Value Observed: 0.201
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.82	α = 79.51
b = 84.559	β = 88.47
c = 145.218	γ = 89.92

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-08-05

Deposition Author(s):

Seo, P.W.

Kim, J.S.

Funding Organization	Location	Grant Number
National Research Foundation (Korea)	Korea, Republic Of	--

Revision History (Full details and data files)

Version 1.0: 2020-08-05
Type: Initial release
Version 1.1: 2021-02-24
Changes: Database references
Version 1.2: 2023-11-22
Changes: Data collection, Database references, Refinement description