2WBI | pdb_00002wbi

Crystal structure of human acyl-CoA dehydrogenase 11

PDB DOI: https://doi.org/10.2210/pdb2WBI/pdb

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

Deposited: 2009-02-28 Released: 2009-05-12
Deposition Author(s): Muniz, J.R.C., Guo, K., Savitsky, P., Roos, A., Yue, W., Pilka, E., von Delft, F., Edwards, A.M., Bountra, C., Arrowsmith, C.H., Weigelt, J., Oppermann, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.248 (Depositor), 0.258 (DCC)
R-Value Work:
0.224 (Depositor), 0.239 (DCC)
R-Value Observed:
0.225 (Depositor)

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 Acyl-Coa Dehydrogenase 11

Muniz, J.R.C., Guo, K., Savitsky, P., Roos, A., Yue, W., Pilka, E., von Delft, F., Edwards, A.M., Bountra, C., Arrowsmith, C.H., Weigelt, J., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 97.19 kDa
Atom Count: 6,232
Modeled Residue Count: 792
Deposited Residue Count: 856
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACYL-COA DEHYDROGENASE FAMILY MEMBER 11	A, B	428	Homo sapiens	Mutation(s): 0 EC: 1.3.8.8
UniProt & NIH Common Fund Data Resources
Find proteins for Q709F0 (Homo sapiens) Explore Q709F0 Go to UniProtKB: Q709F0
PHAROS: Q709F0 GTEx: ENSG00000240303
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q709F0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain J [auth B]	C [auth A], J [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain K [auth B]	D [auth A], K [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain K [auth B]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain L [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B]	UNKNOWN ATOM OR ION X		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.248 (Depositor), 0.258 (DCC)
R-Value Work: 0.224 (Depositor), 0.239 (DCC)
R-Value Observed: 0.225 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.089	α = 90
b = 128.089	β = 90
c = 129.91	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: 2009-05-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-05-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2012-12-05
Changes: Database references, Structure summary
Version 1.3: 2018-01-24
Changes: Database references
Version 1.4: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other, Refinement description