2A5J | pdb_00002a5j

Crystal Structure of Human RAB2B

PDB DOI: https://doi.org/10.2210/pdb2A5J/pdb

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

Deposited: 2005-06-30 Released: 2005-07-19
Deposition Author(s): Dong, A., Wang, J., Shen, Y., 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: 1.50 Å
R-Value Free:
0.225 (Depositor), 0.220 (DCC)
R-Value Work:
0.195 (Depositor), 0.190 (DCC)
R-Value Observed:
0.196 (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

Crystal structure of human RAB2B

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

To be published.

Macromolecule Content

Total Structure Weight: 22.22 kDa
Atom Count: 1,717
Modeled Residue Count: 177
Deposited Residue Count: 191
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Rab-2B	A	191	Homo sapiens	Mutation(s): 0 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WUD1 (Homo sapiens) Explore Q8WUD1 Go to UniProtKB: Q8WUD1
PHAROS: Q8WUD1 GTEx: ENSG00000129472
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8WUD1
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 C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.225 (Depositor), 0.220 (DCC)
R-Value Work: 0.195 (Depositor), 0.190 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.104	α = 90
b = 54.732	β = 90
c = 70.765	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-07-19

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2005-07-19
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2023-08-23
Changes: Data collection, Database references, Derived calculations, Refinement description

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Deposit Data

Help and Resources

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Crystal Structure of Human RAB2B

Crystal structure of human RAB2B

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations