MolNFT v1 · #119852 · protein

Transaminase with L-ala

5GHF · Aminotransferase class-III: “Transaminase with L-ala”. X-ray diffraction, 1 ligand (PMP), 6 pockets (best druggability 0.75). MolNFT v1 #119852 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5GHF
Type: protein
Length: 855 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aminotransferase class-III
UniProt: A6WVC6
Ligands: PMP
Pockets: 6 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Aminotransferase class-III	protein	431	44% helix, 18% strand	A6WVC6
B	Aminotransferase class-III	protein	424	43% helix, 18% strand	A6WVC6

Ligands and binding sites

PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · chains A, B

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	630	0.75	0.82	80	PMP
2	677	0.72	0.79	70	empty
3	164	0.47	0.76	23	empty
4	65	0.30	0.74	17	empty
5	63	0.30	0.74	13	empty

Interfaces

1 interface between chains.

A–B · 4075 Å² buried · 62 hydrogen bonds · protein-protein

Compared structures

5GHF · Transaminase with L-ala · 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 A6WVC6
Elsewhere: RCSB PDB 5GHF · PDBe 5GHF · UniProt A6WVC6

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