MolNFT v1 · #151110 · protein

Crystal structure of human RAB38 in complex with GTP

6HDU · RAS-related protein rab-38: “Crystal structure of human RAB38 in complex with GTP”. X-ray diffraction, 2 ligands (GTP, MG), 6 pockets (best druggability 0.76). MolNFT v1 #151110 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 6HDU
Type: protein
Length: 685 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RAS-related protein rab-38
UniProt: P57729
Ligands: GTP, MG
Pockets: 6 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 34% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RAS-related protein rab-38	protein	172	34% helix, 30% strand	P57729
B	RAS-related protein rab-38	protein	170	32% helix, 30% strand	P57729
C	RAS-related protein rab-38	protein	170	34% helix, 31% strand	P57729
D	RAS-related protein rab-38	protein	173	36% helix, 29% strand	P57729

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · 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

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	1137	0.76	0.79	87	empty
2	377	0.67	0.80	46	GTP, MG
3	155	0.55	0.81	28	GTP, MG
4	147	0.54	0.81	27	GTP, MG
5	149	0.53	0.80	28	GTP, MG

Interfaces

6 interfaces between chains.

C–D · 611 Å² buried · 1 hydrogen bond · protein-protein
A–B · 484 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 375 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 245 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 89 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6HDU · Crystal structure of human Rab38 in complex with GTP · the same entry in another collection · chain D against D, TM-score 1.00
P57729 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-38 (P57729) · a predicted model of the same protein · chain C against A, TM-score 0.99

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 P57729
Elsewhere: RCSB PDB 6HDU · PDBe 6HDU · UniProt P57729

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