3C5C

Crystal structure of human Ras-like, family 12 protein in complex with GDP

PDB DOI: https://doi.org/10.2210/pdb3C5C/pdb

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

Deposited: 2008-01-31 Released: 2008-02-12
Deposition Author(s): Shen, L., Tong, Y., Tempel, W., Loppnau, P., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.238 (Depositor), 0.240 (DCC)
R-Value Work:
0.202 (Depositor), 0.200 (DCC)
R-Value Observed:
0.203 (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 Ras-like, family 12 protein in complex with GDP.

Shen, L., Tong, Y., Tempel, W., Loppnau, P., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H.

To be published.

Macromolecule Content

Total Structure Weight: 87.66 kDa
Atom Count: 5,532
Modelled Residue Count: 659
Deposited Residue Count: 748
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-like protein 12	A, B, C, D	187	Homo sapiens	Mutation(s): 0 Gene Names: RASL12, RIS EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NYN1 (Homo sapiens) Explore Q9NYN1 Go to UniProtKB: Q9NYN1
PHAROS: Q9NYN1 GTEx: ENSG00000103710
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NYN1
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain Q [auth D] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth D]	G [auth A], K [auth B], N [auth C], Q [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth D] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain P [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D]	E [auth A] F [auth A] I [auth B] J [auth B] L [auth C] E [auth A], F [auth A], I [auth B], J [auth B], L [auth C], M [auth C], P [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain P [auth D]
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain O [auth C] SDF format, chain R [auth D] MOL2 format, chain H [auth A] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] mmCIF format, chain H [auth A] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D]	H [auth A], O [auth C], R [auth D]	UNKNOWN ATOM OR ION X		Interactions Focus chain H [auth A] Focus chain O [auth C] Focus chain R [auth D] Interactions & Density Focus chain H [auth A] Focus chain O [auth C] Focus chain R [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.238 (Depositor), 0.240 (DCC)
R-Value Work: 0.202 (Depositor), 0.200 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.04	α = 101.46
b = 66.436	β = 90.03
c = 71.943	γ = 89.89

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-02-12

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2008-02-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2020-10-21
Changes: Data collection, Database references, Derived calculations
Version 1.4: 2023-08-30
Changes: Data collection, Database references, Refinement description