2NZJ | pdb_00002nzj

The crystal structure of REM1 in complex with GDP

PDB DOI: https://doi.org/10.2210/pdb2NZJ/pdb

Deposited: 2006-11-23 Released: 2006-12-12
Deposition Author(s): Turnbull, A.P., Papagrigoriou, E., Ugochukwu, E., Elkins, J.M., Soundararajan, M., Yang, X., Gorrec, F., Umeano, C., Salah, E., Burgess, N., Johansson, C., Berridge, G., Gileadi, O., Bray, J., Marsden, B., Watts, S., von Delft, F., Weigelt, J., Edwards, A., Arrowsmith, C.H., Sundstrom, M., Doyle, D., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.280 (Depositor), 0.276 (DCC)
R-Value Work:
0.225 (Depositor), 0.224 (DCC)
R-Value Observed:
0.227 (Depositor)

Starting Models: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

The crystal structure of REM1 in complex with GDP

Turnbull, A.P., Papagrigoriou, E., Ugochukwu, E., Elkins, J.M., Soundararajan, M., Yang, X., Gorrec, F., Umeano, C., Salah, E., Burgess, N., Johansson, C., Berridge, G., Gileadi, O., Bray, J., Marsden, B., Watts, S., von Delft, F., Weigelt, J., Edwards, A., Arrowsmith, C.H., Sundstrom, M., Doyle, D.

To be published.

Macromolecule Content

Total Structure Weight: 79.92 kDa
Atom Count: 4,785
Modeled Residue Count: 629
Deposited Residue Count: 700
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-binding protein REM 1	A, B, C, D	175	Homo sapiens	Mutation(s): 0 Gene Names: REM1, GES, REM
UniProt & NIH Common Fund Data Resources
Find proteins for O75628 (Homo sapiens) Explore O75628 Go to UniProtKB: O75628
PHAROS: O75628 GTEx: ENSG00000088320
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O75628
Sequence Annotations Expand
Reference Sequence

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 N [auth D] SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain N [auth D] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain N [auth D] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A], J [auth B], L [auth C], N [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain I [auth B] Interactions & Density Focus chain F [auth A] Focus chain I [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain K [auth C] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain M [auth D] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain M [auth D] mmCIF format, chain K [auth C] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], K [auth C], M [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.280 (Depositor), 0.276 (DCC)
R-Value Work: 0.225 (Depositor), 0.224 (DCC)
R-Value Observed: 0.227 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.64	α = 90
b = 102.284	β = 90
c = 165.565	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2006-12-12

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2006-12-12
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description