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Crystal structure of the RAP1GAP catalytic domain

Analyse Crystal structure of the RAP1GAP catalytic domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1SRQ
Type: protein
Length: 1,024 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GTPase-activating protein 1
UniProt: P47736
Ligands: SO4
Pockets: 12 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 31% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	GTPase-activating protein 1	protein	330	32% helix, 26% strand	P47736
B	GTPase-activating protein 1	protein	304	31% helix, 26% strand	P47736
C	GTPase-activating protein 1	protein	324	31% helix, 27% strand	P47736
D	GTPase-activating protein 1	protein	66	24% helix, 15% strand	P47736

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains A, C
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, C

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

Pockets

12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	98	0.76	0.97	33	empty
2	198	0.69	0.87	44	empty
3	222	0.60	0.81	29	MPD
4	236	0.54	0.77	31	MPD
5	273	0.52	0.75	30	empty

Interfaces

4 interfaces between chains.

A–B · 1237 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 1045 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 218 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 30 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

1SRQ · Crystal Structure of the Rap1GAP catalytic domain · the same entry in another collection · chain D against D, TM-score 1.00
P47736 · AlphaFold monomer V2.0 prediction for RAP1 GTPase-activating protein 1 (P47736) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 P47736
Elsewhere: RCSB PDB 1SRQ · PDBe 1SRQ · UniProt P47736

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