3NRU | pdb_00003nru

Ligand binding domain of EPHA7

PDB DOI: https://doi.org/10.2210/pdb3NRU/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2010-06-30 Released: 2010-12-08
Deposition Author(s): Walker, J.R., Yermekbayeva, L., Seitova, A., Kania, J., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.269 (Depositor), 0.260 (DCC)
R-Value Work:
0.235 (Depositor), 0.229 (DCC)
R-Value Observed:
0.237 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Ephrin A7 ligand binding domain

Walker, J.R., Yermekbayeva, L., Seitova, A., Kania, J., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S.

To be published.

Macromolecule Content

Total Structure Weight: 261.78 kDa
Atom Count: 15,958
Modeled Residue Count: 1,902
Deposited Residue Count: 2,244
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ephrin receptor	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	187	Homo sapiens	Mutation(s): 0 Gene Names: EPHA7 EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15375 (Homo sapiens) Explore Q15375 Go to UniProtKB: Q15375
PHAROS: Q15375 GTEx: ENSG00000135333
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15375
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain Q [auth B] SDF format, chain S [auth C] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain V [auth G] SDF format, chain W [auth G] SDF format, chain X [auth J] SDF format, chain P [auth B] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain V [auth G] MOL2 format, chain W [auth G] MOL2 format, chain X [auth J] MOL2 format, chain P [auth B] mmCIF format, chain M [auth A] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D] mmCIF format, chain V [auth G] mmCIF format, chain W [auth G] mmCIF format, chain X [auth J] mmCIF format, chain P [auth B]	M [auth A] O [auth B] P [auth B] Q [auth B] S [auth C] M [auth A], O [auth B], P [auth B], Q [auth B], S [auth C], T [auth D], U [auth D], V [auth G], W [auth G], X [auth J]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth G] Focus chain W [auth G] Focus chain X [auth J] Interactions & Density Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth G] Focus chain W [auth G] Focus chain X [auth J]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain R [auth C] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C]	N [auth B], R [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain N [auth B] Focus chain R [auth C] Interactions & Density Focus chain N [auth B] Focus chain R [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.269 (Depositor), 0.260 (DCC)
R-Value Work: 0.235 (Depositor), 0.229 (DCC)
R-Value Observed: 0.237 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.617	α = 90
b = 140.699	β = 90
c = 143.783	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-12-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-12-08
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-11-06
Changes: Structure summary