2JIF | pdb_00002jif

Structure of human short-branched chain acyl-CoA dehydrogenase (ACADSB)

PDB DOI: https://doi.org/10.2210/pdb2JIF/pdb

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

Deposited: 2007-02-28 Released: 2007-04-03
Deposition Author(s): Pike, A.C.W., Hozjan, V., Smee, C., Niesen, F.H., Kavanagh, K.L., Umeano, C., Turnbull, A.P., von Delft, F., Weigelt, J., Edwards, A., Arrowsmith, C.H., Sundstrom, M., Oppermann, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.209 (Depositor), 0.216 (DCC)
R-Value Work:
0.184 (Depositor), 0.191 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of Human Short-Branched Chain Acyl-Coa Dehydrogenase

Pike, A.C.W., Hozjan, V., Smee, C., Niesen, F.H., Kavanagh, K.L., Umeano, C., Turnbull, A.P., von Delft, F., Weigelt, J., Edwards, A., Arrowsmith, C.H., Sundstrom, M., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 185.03 kDa
Atom Count: 13,144
Modeled Residue Count: 1,516
Deposited Residue Count: 1,616
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SHORT/BRANCHED CHAIN SPECIFIC ACYL-COA DEHYDROGENASE	A, B, C, D	404	Homo sapiens	Mutation(s): 0 EC: 1.3.99 (PDB Primary Data), 1.3.8.5 (UniProt), 1.3.8.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P45954 (Homo sapiens) Explore P45954 Go to UniProtKB: P45954
PHAROS: P45954 GTEx: ENSG00000196177
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P45954
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COS Query on COS Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain V [auth D] SDF format, chain Q [auth C] SDF format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain V [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain V [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain K [auth B]	F [auth A], K [auth B], Q [auth C], V [auth D]	COENZYME A PERSULFIDE C₂₁ H₃₆ N₇ O₁₆ P₃ S₂ REVPHPVBPSIEKM-IBOSZNHHSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain V [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain V [auth D]
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain P [auth C] SDF format, chain U [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain P [auth C] MOL2 format, chain U [auth D] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain P [auth C] mmCIF format, chain U [auth D]	E [auth A], J [auth B], P [auth C], U [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain P [auth C] Focus chain U [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain P [auth C] Focus chain U [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain R [auth C] SDF format, chain Z [auth D] SDF format, chain Y [auth D] SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain R [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain R [auth C] mmCIF format, chain Z [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain G [auth A]	G [auth A] L [auth B] R [auth C] W [auth D] X [auth D] G [auth A], L [auth B], R [auth C], W [auth D], X [auth D], Y [auth D], Z [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain O [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain N [auth B] SDF format, chain I [auth A] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain O [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain N [auth B] MOL2 format, chain I [auth A] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain O [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain N [auth B] mmCIF format, chain I [auth A]	AA [auth D] BA [auth D] CA [auth D] H [auth A] I [auth A] AA [auth D], BA [auth D], CA [auth D], H [auth A], I [auth A], M [auth B], N [auth B], O [auth B], S [auth C], T [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth C] Focus chain T [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth C] Focus chain T [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.209 (Depositor), 0.216 (DCC)
R-Value Work: 0.184 (Depositor), 0.191 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.245	α = 90
b = 150.245	β = 90
c = 201.586	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-04-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-04-03
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2018-01-24
Changes: Database references, Structure summary
Version 1.3: 2023-12-13
Changes: Data collection, Database references, Other, Refinement description