2VIG | pdb_00002vig

Crystal structure of human short-chain acyl CoA dehydrogenase

PDB DOI: https://doi.org/10.2210/pdb2VIG/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-11-30 Released: 2007-12-25
Deposition Author(s): Pike, A.C.W., Pantic, N., Parizotto, E., Gileadi, O., Ugochukwu, E., von Delft, F., Weigelt, J., Arrowsmith, C.H., Edwards, A., Oppermann, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.231 (Depositor), 0.239 (DCC)
R-Value Work:
0.198 (Depositor), 0.205 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure of Human Short-Chain Acyl Coa Dehydrogenase

Pike, A.C.W., Pantic, N., Parizotto, E., Gileadi, O., Ugochukwu, E., von Delft, F., Weigelt, J., Arrowsmith, C.H., Edwards, A., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 348.33 kDa
Atom Count: 24,035
Modeled Residue Count: 3,007
Deposited Residue Count: 3,128
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SHORT-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE,	A, B, C, D, E A, B, C, D, E, F, G, H	391	Homo sapiens	Mutation(s): 0 EC: 1.3.99.2 (PDB Primary Data), 1.3.8.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P16219 (Homo sapiens) Explore P16219 Go to UniProtKB: P16219
PHAROS: P16219 GTEx: ENSG00000122971
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P16219
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COS Query on COS Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain Y [auth F] SDF format, chain Q [auth D] SDF format, chain DA [auth G] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain Y [auth F] MOL2 format, chain Q [auth D] MOL2 format, chain DA [auth G] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain Y [auth F] mmCIF format, chain Q [auth D] mmCIF format, chain DA [auth G]	DA [auth G], L [auth B], O [auth C], Q [auth D], Y [auth F]	COENZYME A PERSULFIDE C₂₁ H₃₆ N₇ O₁₆ P₃ S₂ REVPHPVBPSIEKM-IBOSZNHHSA-N		Interactions Focus chain DA [auth G] Focus chain L [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain Y [auth F] Interactions & Density Focus chain DA [auth G] Focus chain L [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain Y [auth F]
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain P [auth D] SDF format, chain X [auth F] SDF format, chain T [auth E] SDF format, chain N [auth C] SDF format, chain K [auth B] SDF format, chain EA [auth H] SDF format, chain CA [auth G] MOL2 format, chain I [auth A] MOL2 format, chain P [auth D] MOL2 format, chain X [auth F] MOL2 format, chain T [auth E] MOL2 format, chain N [auth C] MOL2 format, chain K [auth B] MOL2 format, chain EA [auth H] MOL2 format, chain CA [auth G] mmCIF format, chain I [auth A] mmCIF format, chain P [auth D] mmCIF format, chain X [auth F] mmCIF format, chain T [auth E] mmCIF format, chain N [auth C] mmCIF format, chain K [auth B] mmCIF format, chain EA [auth H] mmCIF format, chain CA [auth G]	CA [auth G] EA [auth H] I [auth A] K [auth B] N [auth C] CA [auth G], EA [auth H], I [auth A], K [auth B], N [auth C], P [auth D], T [auth E], X [auth F]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain CA [auth G] Focus chain EA [auth H] Focus chain I [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain T [auth E] Focus chain X [auth F] Interactions & Density Focus chain CA [auth G] Focus chain EA [auth H] Focus chain I [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain T [auth E] Focus chain X [auth F]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain FA [auth H] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain U [auth E] SDF format, chain Z [auth F] SDF format, chain W [auth E] SDF format, chain V [auth E] SDF format, chain M [auth B] SDF format, chain J [auth A] SDF format, chain GA [auth H] SDF format, chain BA [auth F] SDF format, chain AA [auth F] MOL2 format, chain FA [auth H] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain U [auth E] MOL2 format, chain Z [auth F] MOL2 format, chain W [auth E] MOL2 format, chain V [auth E] MOL2 format, chain M [auth B] MOL2 format, chain J [auth A] MOL2 format, chain GA [auth H] MOL2 format, chain BA [auth F] MOL2 format, chain AA [auth F] mmCIF format, chain FA [auth H] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D] mmCIF format, chain U [auth E] mmCIF format, chain Z [auth F] mmCIF format, chain W [auth E] mmCIF format, chain V [auth E] mmCIF format, chain M [auth B] mmCIF format, chain J [auth A] mmCIF format, chain GA [auth H] mmCIF format, chain BA [auth F] mmCIF format, chain AA [auth F]	AA [auth F] BA [auth F] FA [auth H] GA [auth H] J [auth A] AA [auth F], BA [auth F], FA [auth H], GA [auth H], J [auth A], M [auth B], R [auth D], S [auth D], U [auth E], V [auth E], W [auth E], Z [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain BA [auth F] Focus chain FA [auth H] Focus chain GA [auth H] Focus chain J [auth A] Focus chain M [auth B] Focus chain R [auth D] Focus chain S [auth D] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth E] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth F] Focus chain FA [auth H] Focus chain GA [auth H] Focus chain J [auth A] Focus chain M [auth B] Focus chain R [auth D] Focus chain S [auth D] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth E] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.231 (Depositor), 0.239 (DCC)
R-Value Work: 0.198 (Depositor), 0.205 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.714	α = 90
b = 157.62	β = 90
c = 260.843	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-12-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-12-25
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2018-01-24
Changes: Database references
Version 1.4: 2023-12-13
Changes: Data collection, Database references, Other, Refinement description