6D0S | pdb_00006d0s

RabGAP domain of human TBC1D22B

PDB DOI: https://doi.org/10.2210/pdb6D0S/pdb
Entry: 6D0S supersedes: 3DZX

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

Deposited: 2018-04-10 Released: 2018-06-06
Deposition Author(s): Tong, Y., Tempel, W., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Park, H., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.239 (Depositor), 0.259 (DCC)
R-Value Work:
0.197 (Depositor), 0.212 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6D0S

This is version 1.1 of the entry. See complete history.

Literature

RabGAP domain of human TBC1D22B

Tong, Y., Tempel, W., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Park, H.

To be published.

Macromolecule Content

Total Structure Weight: 41.87 kDa
Atom Count: 2,267
Modeled Residue Count: 286
Deposited Residue Count: 346
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TBC1 domain family member 22B	A	346	Homo sapiens	Mutation(s): 0 Gene Names: TBC1D22B, C6orf197
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NU19 (Homo sapiens) Explore Q9NU19 Go to UniProtKB: Q9NU19
PHAROS: Q9NU19 GTEx: ENSG00000065491
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NU19
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain J [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain J [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain J [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	UNKNOWN ATOM OR ION X		Interactions Focus chain C [auth A] Focus chain D [auth A] 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 J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] 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 J [auth A] Focus chain K [auth A] Focus chain L [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.239 (Depositor), 0.259 (DCC)
R-Value Work: 0.197 (Depositor), 0.212 (DCC)
R-Value Observed: 0.199 (Depositor)

Diffraction Data:

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.015	α = 90
b = 78.015	β = 90
c = 217.699	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
XDSCONV	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2018-06-06

Deposition Author(s):

Arrowsmith, C.H.

Structural Genomics Consortium (SGC)

This entry supersedes: 3DZX

Revision History (Full details and data files)

Version 1.0: 2018-06-06
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.