Research workbench

EPHA2 lbd in complex with ba-wla-yrpkbio peptide

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

PDB: 6NK1
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-yrpkbio
EC: 2.7.10.1
UniProt: P29317
Pockets: 3 · best druggability 0.67

Structure

x-ray diffraction · 3 distinct chains · 10% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ephrin type-a receptor 2 (EC 2.7.10.1)	protein	181	10% helix, 45% strand	P29317
B	Ephrin type-a receptor 2 (EC 2.7.10.1)	protein	174	10% helix, 46% strand	P29317
C, D	Ba-wla-yrpkbio	protein	14	0% helix, 21% strand	—

Ligands and binding sites

ACT · Acetate ion · additive · 2 copies · chains B
GOL · Glycerol · additive · chains B

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	469	0.67	0.79	51	empty
2	186	0.56	0.79	21	empty
3	176	0.54	0.79	23	empty

Interfaces

5 interfaces between chains.

B–D · 932 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 894 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 604 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 165 Å² buried · 1 hydrogen bond · protein-protein
A–D · 112 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

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

Compared structures

6NK1 · EphA2 LBD in complex with bA-WLA-YRPKbio 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 0.97

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 6NK1 · PDBe 6NK1 · UniProt P29317

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