MolNFT v1 · #86428 · protein

Structure of the atypical C1 domain of mgcracgap

4B6D · Rac GTPase-activating protein 1: “Structure of the atypical C1 domain of mgcracgap”. X-ray diffraction, 1 ligand (ZN), 6 pockets (best druggability 0.77). MolNFT v1 #86428 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4B6D
Type: protein
Length: 354 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rac GTPase-activating protein 1
UniProt: Q9H0H5
Ligands: ZN
Pockets: 6 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 10% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D, F	Rac GTPase-activating protein 1	protein	60	10% helix, 32% strand	Q9H0H5
B, E	Rac GTPase-activating protein 1	protein	57	11% helix, 28% strand	Q9H0H5

Ligands and binding sites

ZN · Zinc ion · metal · 12 copies · chains A, B, C, D, E, F
GOL · Glycerol · additive · chains A

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	743	0.77	0.81	66	GOL
2	393	0.77	0.86	57	empty
3	112	0.49	0.80	21	empty
4	63	0.39	0.80	18	empty
5	72	0.30	0.74	16	empty

Interfaces

12 interfaces between chains.

A–F · 403 Å² buried · 4 hydrogen bonds · protein-protein
D–F · 382 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 374 Å² buried · 4 hydrogen bonds · protein-protein
E–F · 363 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 353 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4B6D · Structure of the atypical C1 domain of MgcRacGAP · the same entry in another collection · chain F against F, TM-score 1.00
Q9H0H5 · AlphaFold monomer V2.0 prediction for rac GTPase-activating protein 1 (Q9H0H5) · a predicted model of the same protein · chain B against A, TM-score 0.91

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 Q9H0H5
Elsewhere: RCSB PDB 4B6D · PDBe 4B6D · UniProt Q9H0H5

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