MolNFT v1 · #29171 · protein

GDP-bound RAB2A GTPase

1Z0A · RAS-related protein rab-2A: “GDP-bound RAB2A GTPase”. X-ray diffraction, 2 ligands (GDP, MG), 5 pockets (best druggability 0.83). MolNFT v1 #29171 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1Z0A
Type: protein
Length: 656 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RAS-related protein rab-2A
UniProt: P61019
Ligands: GDP, MG
Pockets: 5 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 35% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RAS-related protein rab-2A	protein	166	35% helix, 29% strand	P61019
B	RAS-related protein rab-2A	protein	163	36% helix, 31% strand	P61019
C	RAS-related protein rab-2A	protein	169	34% helix, 28% strand	P61019
D	RAS-related protein rab-2A	protein	158	35% helix, 34% strand	P61019

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	895	0.83	0.85	125	MG, GDP
2	76	0.42	0.80	18	empty
3	85	0.39	0.77	17	empty
4	83	0.37	0.77	21	empty
5	102	0.36	0.74	22	MG

Interfaces

5 interfaces between chains.

B–C · 835 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 739 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 732 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 584 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 379 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

1Z0A · GDP-Bound Rab2A GTPase · the same entry in another collection · chain D against D, TM-score 1.00
P61019 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-2A (P61019) · a predicted model of the same protein · chain D 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 P61019
Elsewhere: RCSB PDB 1Z0A · PDBe 1Z0A · UniProt P61019

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