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Crystal structure of SH3BP5-Rab11a

Analyse Crystal structure of SH3BP5-Rab11a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6IXV
Type: protein
Length: 1,570 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.8
Source: Homo sapiens
Molecule: SH3 domain-binding protein 5; Ras-related protein Rab-11A
UniProt: O60239, P62491
Ligands: PO4
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · resolution 3.8 · 7 distinct chains · 66% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	SH3 domain-binding protein 5	protein	224	91% helix, 0% strand	O60239
B	SH3 domain-binding protein 5	protein	226	93% helix, 0% strand	O60239
C	SH3 domain-binding protein 5	protein	222	86% helix, 0% strand	O60239
D	SH3 domain-binding protein 5	protein	226	86% helix, 0% strand	O60239
E, F	Ras-related protein Rab-11A	protein	170	28% helix, 26% strand	P62491
G	Ras-related protein Rab-11A	protein	165	23% helix, 26% strand	P62491
H	Ras-related protein Rab-11A	protein	167	23% helix, 25% strand	P62491

Ligands and binding sites

PO4 · Phosphate ion · ion · 3 copies · chains E, F, H

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

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	912	0.80	0.82	70	empty
2	1001	0.80	0.81	92	empty
3	783	0.80	0.83	69	empty
4	58	0.70	0.96	19	empty
5	712	0.65	0.74	65	empty

Interfaces

11 interfaces between chains.

A–D · 1593 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 1560 Å² buried · 17 hydrogen bonds · protein-protein
B–F · 1301 Å² buried · 17 hydrogen bonds · protein-protein
D–H · 1248 Å² buried · 11 hydrogen bonds · protein-protein
A–E · 1235 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

6IXV · Crystal structure of SH3BP5-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 B 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 H against A, TM-score 0.86

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

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