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Transaminase from pseudomonas fluorescens

Analyse Transaminase from pseudomonas fluorescens in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6S54
Type: protein
Length: 1,799 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aspartate aminotransferase family protein
UniProt: A0A2S8XV37
Ligands: PLP, SO4
Pockets: 14 · best druggability 0.87

Structure

x-ray diffraction · 4 distinct chains · 42% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Aspartate aminotransferase family protein	protein	453	43% helix, 19% strand	A0A2S8XV37
B	Aspartate aminotransferase family protein	protein	450	42% helix, 20% strand	A0A2S8XV37
C	Aspartate aminotransferase family protein	protein	447	42% helix, 20% strand	A0A2S8XV37
D	Aspartate aminotransferase family protein	protein	449	42% helix, 20% strand	A0A2S8XV37

Ligands and binding sites

PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 2 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains A, D, B, C

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

Pockets

14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	410	0.87	0.96	76	empty
2	1010	0.79	0.80	87	PLP
3	1057	0.78	0.80	86	PLP
4	954	0.78	0.80	86	PLP
5	981	0.77	0.79	92	PLP

Interfaces

6 interfaces between chains.

A–B · 5611 Å² buried · 79 hydrogen bonds · protein-protein
C–D · 5530 Å² buried · 68 hydrogen bonds · protein-protein
A–D · 1162 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 1153 Å² buried · 14 hydrogen bonds · protein-protein
B–D · 195 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

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

Compared structures

6S54 · Transaminase from Pseudomonas fluorescens · 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 A0A2S8XV37
Elsewhere: RCSB PDB 6S54 · PDBe 6S54 · UniProt A0A2S8XV37

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