Research workbench

EPHA2 lbd in complex with ba-wla-yrpk bio peptide

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

PDB: 6NK2
Type: protein
Length: 383 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ephrin type-a receptor 2; Ba-wla-yprkbio peptide
EC: 2.7.10.1
UniProt: P29317
Pockets: 3 · best druggability 0.69

Structure

x-ray diffraction · 4 distinct chains · 8% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ephrin type-a receptor 2 (EC 2.7.10.1)	protein	177	8% helix, 46% strand	P29317
B	Ephrin type-a receptor 2 (EC 2.7.10.1)	protein	179	9% helix, 46% strand	P29317
C	Ba-wla-yprkbio peptide	protein	14	0% helix, 14% strand	—
D	Ba-wla-yprkbio peptide	protein	13	0% helix, 23% strand	—

Ligands and binding sites

PEG · Di(hydroxyethyl)ether · additive · chains A

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

Pockets

3 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	348	0.69	0.82	43	empty
2	536	0.67	0.78	53	empty
3	115	0.44	0.78	18	empty

Interfaces

5 interfaces between chains.

A–C · 865 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 848 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 601 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 126 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 93 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 1 modified (disulfide, nonstandard).

Compared structures

6NK2 · EphA2 LBD in complex with bA-WLA-YRPK bio 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 A against A, TM-score 0.97

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 6NK2 · PDBe 6NK2 · UniProt P29317

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