MolNFT v1 · #190648 · protein

The complex of nanobody RH57 binding to GTP-bound rhoa active form

7XQV: “The complex of nanobody RH57 binding to GTP-bound rhoa active form”. X-ray diffraction, 3 ligands (ALA, GNP, MG), 3 pockets (best druggability 0.68). MolNFT v1 #190648 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7XQV
Type: protein
Length: 279 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rhoa; RH57
Ligands: ALA, GNP, MG
Pockets: 3 · best druggability 0.68

Structure

x-ray diffraction · 2 distinct chains · 22% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Rhoa	protein	163	35% helix, 28% strand	—
B	RH57	protein	116	3% helix, 57% strand	—

Ligands and binding sites

ALA · Alanine · ligand · chains A
GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A
MG · Magnesium ion · metal · chains A

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

Pockets

3 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	388	0.68	0.80	47	GNP, MG
2	59	0.41	0.81	14	empty
3	94	0.38	0.76	15	empty

Interfaces

1 interface between chains.

A–B · 889 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

7XQV · The complex of nanobody Rh57 binding to GTP-bound RhoA active form · the same entry in another collection · chain B against B, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 7XQV · PDBe 7XQV

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