Research workbench

EPHA2 lbd in complex with ba-wla-yam peptide

Analyse EPHA2 lbd in complex with ba-wla-yam peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6NK0
Type: protein
Length: 381 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ephrin type-a receptor 2; Ba-wla-yam
EC: 2.7.10.1
UniProt: P29317
Ligands: ACA, NH2
Pockets: 5 · best druggability 0.56

Structure

x-ray diffraction · 3 distinct chains · 9% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ephrin type-a receptor 2 (EC 2.7.10.1)	protein	178	10% helix, 46% strand	P29317
B	Ephrin type-a receptor 2 (EC 2.7.10.1)	protein	181	8% helix, 45% strand	P29317
C, D	Ba-wla-yam	protein	11	0% helix, 18% strand	—

Ligands and binding sites

ACA · 6-aminohexanoic acid · ligand · chains A
NH2 · Amino group · ion · 2 copies · chains C, B, D
GOL · Glycerol · additive · 3 copies · chains A, B
EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
PEG · Di(hydroxyethyl)ether · additive · chains B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	168	0.56	0.81	26	empty
2	102	0.54	0.83	17	empty
3	100	0.40	0.77	18	empty
4	88	0.37	0.76	15	GOL
5	52	0.29	0.76	12	empty

Interfaces

3 interfaces between chains.

A–B · 962 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 844 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 837 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 2 modified (disulfide, nonstandard).

Compared structures

6NK0 · EphA2 LBD in complex with bA-WLA-Yam peptide · the same entry in another collection · chain A against A, TM-score 1.00
P29317 · AlphaFold monomer V2.0 prediction for ephrin type-a receptor 2 (P29317) · a predicted model of the same protein · chain B against A, TM-score 0.96

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P29317
Elsewhere: RCSB PDB 6NK0 · PDBe 6NK0 · UniProt P29317

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