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PAB0955 crystal structure : a GTPase in GDP bound form from pyrococcus abyssi

Analyse PAB0955 crystal structure : a GTPase in GDP bound form from pyrococcus abyssi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1YRA
Type: protein
Length: 521 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP(GTP)BINDING protein
Ligands: GDP
Pockets: 7 · best druggability 0.65

Structure

x-ray diffraction · 2 distinct chains · 52% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ATP(GTP)BINDING protein	protein	260	50% helix, 12% strand	—
B	ATP(GTP)BINDING protein	protein	261	54% helix, 12% strand	—

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	365	0.65	0.80	47	empty
2	443	0.65	0.78	58	empty
3	243	0.54	0.77	33	GDP
4	92	0.42	0.78	15	empty
5	50	0.38	0.81	15	empty

Interfaces

1 interface between chains.

A–B · 2296 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

1YRA · PAB0955 crystal structure : a GTPase in GDP bound form from Pyrococcus abyssi · the same entry in another collection · chain A against A, 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 1YRA · PDBe 1YRA

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