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Crystal structure of rab GTPase SEC4P mutant - S29V

Analyse Crystal structure of rab GTPase SEC4P mutant - S29V in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4Z8Y
Type: protein
Length: 327 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RAS-related protein SEC4
UniProt: P07560
Ligands: GDP, ZN, MG
Pockets: 4 · best druggability 0.42

Structure

x-ray diffraction · 2 distinct chains · 36% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RAS-related protein SEC4	protein	160	36% helix, 28% strand	P07560
B	RAS-related protein SEC4	protein	167	36% helix, 29% strand	P07560

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
ZN · Zinc ion · metal · 3 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	58	0.42	0.82	20	MG
2	117	0.39	0.75	30	GDP, MG
3	116	0.37	0.74	20	empty
4	68	0.29	0.73	17	empty

Interfaces

1 interface between chains.

A–B · 254 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

4Z8Y · Crystal structure of Rab GTPase Sec4p mutant - S29V · the same entry in another collection · chain B against B, TM-score 1.00
P07560 · AlphaFold monomer V2.0 prediction for RAS-related protein SEC4 (P07560) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P07560
Elsewhere: RCSB PDB 4Z8Y · PDBe 4Z8Y · UniProt P07560

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