2WH5 | pdb_00002wh5

Crystal structure of human acyl-CoA binding domain 4 complexed with stearoyl-CoA

PDB DOI: https://doi.org/10.2210/pdb2WH5/pdb

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

Deposited: 2009-04-30 Released: 2009-07-28
Deposition Author(s): Yue, W.W., Shafqat, N., Ugochukwu, E., Savitsky, P., Johansson, C., Salah, E., Roos, A.K., Chaikuad, A., von Delft, F., Arrowsmith, C., Weigelt, J., Edwards, A., Bountra, C., Oppermann, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.236 (Depositor), 0.220 (DCC)
R-Value Work:
0.206 (Depositor), 0.190 (DCC)
R-Value Observed:
0.207 (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 Acyl-Coa Binding Domain 4

Shafqat, N., Yue, W.W., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 82.32 kDa
Atom Count: 4,951
Modeled Residue Count: 536
Deposited Residue Count: 636
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACYL-COA-BINDING DOMAIN-CONTAINING PROTEIN 4	A, B, C, D, E A, B, C, D, E, F	106	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NC06 (Homo sapiens) Explore Q8NC06 Go to UniProtKB: Q8NC06
PHAROS: Q8NC06 GTEx: ENSG00000181513
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8NC06
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ST9 Query on ST9 Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] SDF format, chain Q [auth E] SDF format, chain T [auth F] SDF format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain T [auth F] MOL2 format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain T [auth F] mmCIF format, chain H [auth A]	H [auth A] J [auth B] L [auth C] N [auth D] Q [auth E] H [auth A], J [auth B], L [auth C], N [auth D], Q [auth E], T [auth F]	STEAROYL-COENZYME A C₃₉ H₇₀ N₇ O₁₇ P₃ S SIARJEKBADXQJG-LFZQUHGESA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain Q [auth E] Focus chain T [auth F] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain Q [auth E] Focus chain T [auth F]
COA Query on COA Download Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain R [auth E] MOL2 format, chain O [auth D] MOL2 format, chain R [auth E] mmCIF format, chain O [auth D] mmCIF format, chain R [auth E]	O [auth D], R [auth E]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain O [auth D] Focus chain R [auth E] Interactions & Density Focus chain O [auth D] Focus chain R [auth E]
STE Query on STE Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth C] SDF format, chain P [auth E] SDF format, chain S [auth F] SDF format, chain M [auth D] SDF format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain K [auth C] MOL2 format, chain P [auth E] MOL2 format, chain S [auth F] MOL2 format, chain M [auth D] MOL2 format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain K [auth C] mmCIF format, chain P [auth E] mmCIF format, chain S [auth F] mmCIF format, chain M [auth D] mmCIF format, chain I [auth B]	G [auth A] I [auth B] K [auth C] M [auth D] P [auth E] G [auth A], I [auth B], K [auth C], M [auth D], P [auth E], S [auth F]	STEARIC ACID C₁₈ H₃₆ O₂ QIQXTHQIDYTFRH-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain P [auth E] Focus chain S [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain P [auth E] Focus chain S [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.236 (Depositor), 0.220 (DCC)
R-Value Work: 0.206 (Depositor), 0.190 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.06	α = 90
b = 95.1	β = 110.28
c = 119.74	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-07-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-07-28
Type: Initial release
Version 1.1: 2012-12-05
Changes: Database references, Derived calculations, Other, Refinement description, Structure summary, Version format compliance
Version 1.2: 2013-09-25
Changes: Advisory, Non-polymer description, Source and taxonomy
Version 1.3: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description

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Deposit Data

Help and Resources

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 2WH5 | pdb_00002wh5

Crystal structure of human acyl-CoA binding domain 4 complexed with stearoyl-CoA

Crystal Structure of Human Acyl-Coa Binding Domain 4

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations