2F7S | pdb_00002f7s

The crystal structure of human Rab27b bound to GDP

PDB DOI: https://doi.org/10.2210/pdb2F7S/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2005-12-01 Released: 2005-12-20
Deposition Author(s): Wang, J., Ismail, S., Shen, Y., Tempel, W., Arrowsmith, C.H., Edwards, A.M., Sundstrom, M., Bochkarev, A., Park, H.W., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.292 (Depositor), 0.294 (DCC)
R-Value Work:
0.245 (Depositor), 0.242 (DCC)
R-Value Observed:
0.248 (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

The crystal structure of human Rab27b

Wang, J., Ismail, S., Shen, Y., Tempel, W., Arrowsmith, C.H., Edwards, A.M., Sundstrom, M., Bochkarev, A., Park, H.W.

To be published.

Macromolecule Content

Total Structure Weight: 49.94 kDa
Atom Count: 2,958
Modeled Residue Count: 355
Deposited Residue Count: 434
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Rab-27B	A, B	217	Homo sapiens	Mutation(s): 0 Gene Names: RAB27B EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for O00194 (Homo sapiens) Explore O00194 Go to UniProtKB: O00194
PHAROS: O00194 GTEx: ENSG00000041353
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O00194
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.292 (Depositor), 0.294 (DCC)
R-Value Work: 0.245 (Depositor), 0.242 (DCC)
R-Value Observed: 0.248 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.469	α = 90
b = 64.023	β = 90
c = 153.32	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2005-12-20

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2005-12-20
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-11-13
Changes: Structure summary

2F7S | pdb_00002f7s

The crystal structure of human Rab27b bound to GDP

Literature

The crystal structure of human Rab27b

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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