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Crystal structure of tetrameric human RABIN8 gef domain

Analyse Crystal structure of tetrameric human RABIN8 gef domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6F6P
Type: protein
Length: 382 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rab-3A-interacting protein
UniProt: Q96QF0
Pockets: 6 · best druggability 0.70

Structure

x-ray diffraction · 3 distinct chains · 98% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Rab-3A-interacting protein	protein	98	98% helix, 0% strand	Q96QF0
B	Rab-3A-interacting protein	protein	97	97% helix, 0% strand	Q96QF0
C	Rab-3A-interacting protein	protein	89	98% helix, 0% strand	Q96QF0

Pockets

6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	430	0.70	0.81	27	empty
2	525	0.67	0.78	42	empty
3	329	0.66	0.81	25	empty
4	96	0.65	0.90	20	empty
5	186	0.59	0.81	20	empty

Interfaces

6 interfaces between chains.

A–B · 1362 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 1228 Å² buried · 1 hydrogen bond · protein-protein
A–C · 1223 Å² buried · 1 hydrogen bond · protein-protein
C–D · 1220 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 386 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6F6P · Crystal structure of tetrameric human Rabin8 GEF domain · the same entry in another collection · chain A against A, TM-score 1.00
Q96QF0 · AlphaFold monomer V2.0 prediction for rab-3A-interacting protein (Q96QF0) · a predicted model of the same protein · chain C against A, TM-score 0.96

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 Q96QF0
Elsewhere: RCSB PDB 6F6P · PDBe 6F6P · UniProt Q96QF0

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