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Crystall structure of pyrococcus protein-A1

Analyse Crystall structure of pyrococcus protein-A1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1GD9
Type: protein
Length: 776 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aspartate aminotransferase
EC: 2.6.1.-
UniProt: O59096
Ligands: PLP
Pockets: 3 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Aspartate aminotransferase (EC 2.6.1.-)	protein	388	46% helix, 14% strand	O59096

Ligands and binding sites

PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B

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

Pockets

3 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	778	0.78	0.82	81	PLP
2	824	0.77	0.81	78	PLP
3	50	0.35	0.80	14	empty

Interfaces

1 interface between chains.

A–B · 2785 Å² buried · 49 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).

Compared structures

1GD9 · Crystall structure of pyrococcus protein-A1 · 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
Every structure of UniProt O59096
Elsewhere: RCSB PDB 1GD9 · PDBe 1GD9 · UniProt O59096

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