MolNFT v1 · #12443 · protein

Crystal structure of the EPHB2-EPHRINB2 complex

1KGY · Ephrin type-B receptor 2: “Crystal structure of the EPHB2-EPHRINB2 complex”. X-ray diffraction, 20 pockets (best druggability 0.69). MolNFT v1 #12443 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1KGY
Type: protein
Length: 1,276 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ephrin type-B receptor 2; Ephrin-B2
EC: 2.7.1.112
UniProt: P54763, P52800
Pockets: 20 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 3% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Ephrin type-B receptor 2 (EC 2.7.1.112)	protein	181	2% helix, 45% strand	P54763
E, F, G, H	Ephrin-B2	protein	138	4% helix, 33% strand	P52800

Pockets

20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	774	0.69	0.76	93	empty
2	176	0.59	0.82	24	empty
3	184	0.57	0.81	26	empty
4	324	0.57	0.76	43	empty
5	174	0.54	0.80	21	empty

Interfaces

9 interfaces between chains.

C–G · 1257 Å² buried · 25 hydrogen bonds · protein-protein
B–F · 1230 Å² buried · 22 hydrogen bonds · protein-protein
A–E · 1220 Å² buried · 22 hydrogen bonds · protein-protein
D–H · 1195 Å² buried · 23 hydrogen bonds · protein-protein
B–G · 598 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

1KGY · Crystal Structure of the EphB2-ephrinB2 complex · the same entry in another collection · chain H against H, TM-score 1.00
P52800 · AlphaFold monomer V2.0 prediction for ephrin-B2 (P52800) · a predicted model of the same protein · chain G 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 P54763
Every structure of UniProt P52800
Elsewhere: RCSB PDB 1KGY · PDBe 1KGY · UniProt P54763 · UniProt P52800

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