2REX

Crystal structure of the effector domain of PLXNB1 bound with Rnd1 GTPase

PDB DOI: https://doi.org/10.2210/pdb2REX/pdb

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

Deposited: 2007-09-27 Released: 2007-11-20
Deposition Author(s): Tong, Y., Tempel, W., Shen, L., Arrowsmith, C.H., Edwards, A.M., Sundstrom, M., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.248
R-Value Work: 0.215
R-Value Observed: 0.216

Starting Models: 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 the effector domain of PLXNB1 bound with Rnd1 GTPase.

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

To be published.

Macromolecule Content

Total Structure Weight: 71.66 kDa
Atom Count: 4,464
Modelled Residue Count: 565
Deposited Residue Count: 636
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plexin-B1	A, C	121	Homo sapiens	Mutation(s): 0 Gene Names: PLXNB1, KIAA0407, PLXN5, SEP
UniProt & NIH Common Fund Data Resources
Find proteins for O43157 (Homo sapiens) Explore O43157 Go to UniProtKB: O43157
PHAROS: O43157 GTEx: ENSG00000164050
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O43157
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Rho-related GTP-binding protein Rho6	B, D	197	Homo sapiens	Mutation(s): 0 Gene Names: RND1, RHO6
UniProt & NIH Common Fund Data Resources
Find proteins for Q92730 (Homo sapiens) Explore Q92730 Go to UniProtKB: Q92730
PHAROS: Q92730 GTEx: ENSG00000172602
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q92730
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GNP Query on GNP Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain K [auth B] MOL2 format, chain DA [auth D] MOL2 format, chain K [auth B] mmCIF format, chain DA [auth D] mmCIF format, chain K [auth B]	DA [auth D], K [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C₁₀ H₁₇ N₆ O₁₃ P₃ UQABYHGXWYXDTK-UUOKFMHZSA-N		Interactions Focus chain DA [auth D] Focus chain K [auth B] Interactions & Density Focus chain DA [auth D] Focus chain K [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain J [auth B] MOL2 format, chain CA [auth D] MOL2 format, chain J [auth B] mmCIF format, chain CA [auth D] mmCIF format, chain J [auth B]	CA [auth D], J [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain J [auth B] Interactions & Density Focus chain CA [auth D] Focus chain J [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain I [auth B] MOL2 format, chain BA [auth D] MOL2 format, chain I [auth B] mmCIF format, chain BA [auth D] mmCIF format, chain I [auth B]	BA [auth D], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain I [auth B] Interactions & Density Focus chain BA [auth D] Focus chain I [auth B]
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain NA [auth D] SDF format, chain P [auth B] SDF format, chain V [auth B] SDF format, chain Y [auth C] SDF format, chain AA [auth C] SDF format, chain E [auth A] SDF format, chain EA [auth D] SDF format, chain F [auth A] SDF format, chain FA [auth D] SDF format, chain G [auth A] SDF format, chain GA [auth D] SDF format, chain HA [auth D] SDF format, chain IA [auth D] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain L [auth B] SDF format, chain LA [auth D] SDF format, chain M [auth B] SDF format, chain MA [auth D] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Z [auth C] MOL2 format, chain H [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain V [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain IA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain L [auth B] MOL2 format, chain LA [auth D] MOL2 format, chain M [auth B] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain H [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain P [auth B] mmCIF format, chain V [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain IA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain KA [auth D] mmCIF format, chain L [auth B] mmCIF format, chain LA [auth D] mmCIF format, chain M [auth B] mmCIF format, chain MA [auth D] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Z [auth C]	AA [auth C] E [auth A] EA [auth D] F [auth A] FA [auth D] AA [auth C], E [auth A], EA [auth D], F [auth A], FA [auth D], G [auth A], GA [auth D], H [auth A], HA [auth D], IA [auth D], JA [auth D], KA [auth D], L [auth B], LA [auth D], M [auth B], MA [auth D], N [auth B], NA [auth D], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth C], X [auth C], Y [auth C], Z [auth C]	UNKNOWN ATOM OR ION X		Interactions Focus chain AA [auth C] Focus chain E [auth A] Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain L [auth B] Focus chain LA [auth D] Focus chain M [auth B] Focus chain MA [auth D] Focus chain N [auth B] Focus chain NA [auth D] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain E [auth A] Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain L [auth B] Focus chain LA [auth D] Focus chain M [auth B] Focus chain MA [auth D] Focus chain N [auth B] Focus chain NA [auth D] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.248
R-Value Work: 0.215
R-Value Observed: 0.216
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.136	α = 90
b = 71.653	β = 128.36
c = 101.885	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-11-20

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2007-11-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-11-20
Changes: Structure summary