MolNFT v1 · #143778 · protein

Crystal structure of EPHA2 with peptide 135E2

6B9L · Ephrin type-a receptor 2: “Crystal structure of EPHA2 with peptide 135E2”. X-ray diffraction, 1 ligand (DUG), 8 pockets (best druggability 0.83). MolNFT v1 #143778 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6B9L
Type: protein
Length: 742 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ephrin type-a receptor 2; Peptide 135E2, (DUG)SAYPDSVPFR; His tag cleaved off
EC: 2.7.10.1
UniProt: P29317
Ligands: DUG
Pockets: 8 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 7% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Ephrin type-a receptor 2 (EC 2.7.10.1)	protein	174	8% helix, 44% strand	P29317
E, F, G, H	Peptide 135E2, (DUG)SAYPDSVPFR	protein	10	0% helix, 30% strand	—
J	His tag cleaved off	protein	6	0% helix, 33% strand	—

Ligands and binding sites

DUG · (3-chloro-4-fluorophenoxy)acetaldehyde · ligand · 4 copies · chains A, E, G, B, F, H, C, D

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

Pockets

8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	597	0.83	0.88	68	DUG
2	439	0.81	0.89	57	DUG
3	489	0.74	0.83	45	empty
4	387	0.61	0.76	34	empty
5	370	0.60	0.76	36	empty

Interfaces

21 interfaces between chains.

A–E · 749 Å² buried · 12 hydrogen bonds · protein-protein
B–F · 744 Å² buried · 11 hydrogen bonds · protein-protein
C–G · 732 Å² buried · 9 hydrogen bonds · protein-protein
D–H · 704 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 662 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 4 covalent (disulfide, covalent ligand).

Compared structures

6B9L · Crystal structure of EphA2 with peptide 135E2 · the same entry in another collection · chain J against J, 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 C 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 6B9L · PDBe 6B9L · UniProt P29317

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