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Crystal structure of the RAB11 gef SH3BP5 bound to nucleotide free RAB11A

Analyse Crystal structure of the RAB11 gef SH3BP5 bound to nucleotide free RAB11A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6DJL
Type: protein
Length: 1,597 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RAS-related protein rab-11A; SH3 domain-binding protein 5
UniProt: P62491, O60239
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 6 distinct chains · 67% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RAS-related protein rab-11A	protein	176	35% helix, 25% strand	P62491
B	SH3 domain-binding protein 5	protein	221	95% helix, 0% strand	O60239
C, D	SH3 domain-binding protein 5	protein	224	88% helix, 0% strand	O60239
E	SH3 domain-binding protein 5	protein	226	95% helix, 0% strand	O60239
F, H	RAS-related protein rab-11A	protein	177	34% helix, 25% strand	P62491
G	RAS-related protein rab-11A	protein	172	35% helix, 26% strand	P62491

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1071	0.76	0.78	81	empty
2	1121	0.75	0.78	81	empty
3	570	0.74	0.82	56	empty
4	791	0.69	0.76	66	empty
5	524	0.67	0.78	42	empty

Interfaces

10 interfaces between chains.

D–E · 1448 Å² buried · 12 hydrogen bonds · protein-protein
E–F · 1315 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 1311 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 1264 Å² buried · 10 hydrogen bonds · protein-protein
D–G · 1237 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

6DJL · Crystal structure of the Rab11 GEF SH3BP5 bound to nucleotide free Rab11A · the same entry in another collection · chain H against H, TM-score 1.00
O60239 · AlphaFold monomer V2.0 prediction for SH3 domain-binding protein 5 (O60239) · a predicted model of the same protein · chain D against A, TM-score 0.91
P62491 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-11A (P62491) · a predicted model of the same protein · chain G against A, TM-score 0.89

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 P62491
Every structure of UniProt O60239
Elsewhere: RCSB PDB 6DJL · PDBe 6DJL · UniProt P62491 · UniProt O60239

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