MolNFT v1 · #119853 · protein

Transaminase W58L with smba

5GHG · Aminotransferase class-III: “Transaminase W58L with smba”. X-ray diffraction, 1 ligand (PMP), 8 pockets (best druggability 0.76). MolNFT v1 #119853 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5GHG
Type: protein
Length: 858 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aminotransferase class-III
UniProt: A6WVC6
Ligands: PMP
Pockets: 8 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Aminotransferase class-III	protein	425	44% helix, 18% strand	A6WVC6
B	Aminotransferase class-III	protein	433	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

8 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	690	0.76	0.81	84	PMP
2	505	0.70	0.80	52	empty
3	117	0.40	0.75	20	empty
4	67	0.35	0.77	14	empty
5	53	0.32	0.77	11	empty

Interfaces

1 interface between chains.

A–B · 4116 Å² buried · 64 hydrogen bonds · protein-protein

Compared structures

5GHG · Transaminase W58L with SMBA · 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 5GHG · PDBe 5GHG · UniProt A6WVC6

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