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Oligomeric structure of the human EPHB2 receptor SAM domain

Analyse Oligomeric structure of the human EPHB2 receptor SAM domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1B4F
Type: protein
Length: 599 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: EPHB2
UniProt: P29323
Pockets: 8 · best druggability 0.72

Structure

x-ray diffraction · 6 distinct chains · 65% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E	EPHB2	protein	74	65% helix, 0% strand	P29323
B	EPHB2	protein	77	64% helix, 0% strand	P29323
D	EPHB2	protein	75	64% helix, 0% strand	P29323
F	EPHB2	protein	77	66% helix, 0% strand	P29323
G	EPHB2	protein	72	64% helix, 0% strand	P29323
H	EPHB2	protein	76	64% helix, 0% strand	P29323

Pockets

8 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	448	0.72	0.82	50	empty
2	530	0.68	0.78	53	empty
3	463	0.67	0.79	51	empty
4	111	0.43	0.77	26	empty
5	83	0.35	0.75	16	empty

Interfaces

10 interfaces between chains.

E–F · 719 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 694 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 674 Å² buried · 8 hydrogen bonds · protein-protein
G–H · 630 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 227 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

1B4F · Oligomeric structure of the human EPHB2 receptor SAM domain · the same entry in another collection · chain H against H, TM-score 1.00
P29323 · AlphaFold monomer V2.0 prediction for ephrin type-B receptor 2 (P29323) · a predicted model of the same protein · chain G against A, TM-score 0.93

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 P29323
Elsewhere: RCSB PDB 1B4F · PDBe 1B4F · UniProt P29323

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