MolNFT v1 · #168344 · protein

Structure of human rubicon rh domain in complex with GTP-bound RAB7

6WCW · RAS-related protein rab-7A: “Structure of human rubicon rh domain in complex with GTP-bound RAB7”. X-ray diffraction, 3 ligands (GTP, ZN, MG), 6 pockets (best druggability 0.74). MolNFT v1 #168344 on GenesisL1: 3D structure, binding…

PDB: 6WCW
Type: protein
Length: 423 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RAS-related protein rab-7A; Run domain beclin-1-interacting and cysteine-rich domain…
UniProt: P51149, Q92622
Ligands: GTP, ZN, MG
Pockets: 6 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	RAS-related protein rab-7A	protein	176	34% helix, 25% strand	P51149
A	Run domain beclin-1-interacting and cysteine-rich domain- containing protein	protein	247	45% helix, 10% strand	Q92622

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · chains B
ZN · Zinc ion · metal · 4 copies · chains A
MG · Magnesium ion · metal · chains B

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	317	0.74	0.86	42	empty
2	166	0.51	0.78	30	GTP
3	96	0.36	0.74	21	empty
4	81	0.34	0.75	22	empty
5	53	0.29	0.75	16	empty

Interfaces

1 interface between chains.

B–A · 962 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

6WCW · Structure of human Rubicon RH domain in complex with GTP-bound Rab7 · the same entry in another collection · chain B against B, TM-score 1.00
P51149 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-7A (P51149) · a predicted model of the same protein · chain B against A, TM-score 0.97
Q92622 · AlphaFold monomer V2.0 prediction for run domain beclin-1-interacting and cysteine-rich… · a predicted model of the same protein · chain A against A, TM-score 0.92

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 P51149
Every structure of UniProt Q92622
Elsewhere: RCSB PDB 6WCW · PDBe 6WCW · UniProt P51149 · UniProt Q92622

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