Research workbench

EphA2 LBD in complex with bA-WLA-YSKbio peptide

Analyse EphA2 LBD in complex with bA-WLA-YSKbio peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6NKP
Type: protein
Length: 377 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.033
Source: Homo sapiens; SYNTHETIC CONSTRUCT
Molecule: Ephrin type-A receptor 2; bA-WLA-YSKbio peptide
EC: 2.7.10.1
UniProt: P29317
Ligands: BTN
Pockets: 4 · best druggability 0.62

Structure

x-ray diffraction · resolution 2.033 · 4 distinct chains · 7% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ephrin type-A receptor 2 (EC 2.7.10.1)	protein	175	8% helix, 46% strand	P29317
B	Ephrin type-A receptor 2 (EC 2.7.10.1)	protein	179	8% helix, 44% strand	P29317
C	bA-WLA-YSKbio peptide	protein	11	0% helix, 18% strand	—
D	bA-WLA-YSKbio peptide	protein	12	0% helix, 17% strand	—

Ligands and binding sites

BTN · Biotin · ligand · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	501	0.62	0.75	39	BTN
2	108	0.45	0.78	24	empty
3	95	0.43	0.78	24	empty
4	58	0.33	0.77	14	empty

Interfaces

3 interfaces between chains.

B–D · 849 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 836 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 764 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

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

Compared structures

6NKP · EPHA2 lbd in complex with ba-wla-yskbio 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 6NKP · PDBe 6NKP · UniProt P29317

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