MolNFT v1 · #146630 · protein

Crystal structure of T110A mutant human glutamate oxaloacetate transaminase 1 (GOT1)

6DNA · Aspartate aminotransferase, cytoplasmic: “Crystal structure of T110A mutant human glutamate oxaloacetate transaminase 1 (GOT1)”. X-ray diffraction, 1 ligand (PLP), 20 pockets (best druggability 0.78). MolNFT v1 #146630 on GenesisL1…

PDB: 6DNA
Type: protein
Length: 2,348 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aspartate aminotransferase, cytoplasmic
EC: 2.6.1.1, 2.6.1.3
UniProt: P17174
Ligands: PLP
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 6 distinct chains · 41% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Aspartate aminotransferase, cytoplasmic (EC 2.6.1.1, 2.6.1.3)	protein	390	41% helix, 14% strand	P17174
B	Aspartate aminotransferase, cytoplasmic (EC 2.6.1.1, 2.6.1.3)	protein	395	41% helix, 13% strand	P17174
C	Aspartate aminotransferase, cytoplasmic (EC 2.6.1.1, 2.6.1.3)	protein	391	43% helix, 14% strand	P17174
D	Aspartate aminotransferase, cytoplasmic (EC 2.6.1.1, 2.6.1.3)	protein	396	40% helix, 14% strand	P17174
E	Aspartate aminotransferase, cytoplasmic (EC 2.6.1.1, 2.6.1.3)	protein	393	37% helix, 13% strand	P17174
F	Aspartate aminotransferase, cytoplasmic (EC 2.6.1.1, 2.6.1.3)	protein	383	42% helix, 13% strand	P17174

Ligands and binding sites

PLP · Pyridoxal-5'-phosphate · ligand · 6 copies · chains A, B, C, D, E, F
PG4 · Tetraethylene glycol · additive · 3 copies · chains A, B, D

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	186	0.78	0.93	26	empty
2	853	0.78	0.81	92	PLP
3	268	0.77	0.89	31	empty
4	158	0.76	0.93	36	PLP
5	85	0.75	0.97	26	PLP

Interfaces

12 interfaces between chains.

A–B · 2394 Å² buried · 46 hydrogen bonds · protein-protein
C–D · 2383 Å² buried · 37 hydrogen bonds · protein-protein
E–F · 2143 Å² buried · 41 hydrogen bonds · protein-protein
C–F · 185 Å² buried · 1 hydrogen bond · protein-protein
B–E · 164 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6DNA · Crystal structure of T110A mutant human Glutamate oxaloacetate transaminase 1 (GOT1) · the same entry in another collection · chain F against F, TM-score 1.00
P17174 · AlphaFold monomer V2.0 prediction for aspartate aminotransferase, cytoplasmic (P17174) · a predicted model of the same protein · chain C against A, TM-score 0.98

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 P17174
Elsewhere: RCSB PDB 6DNA · PDBe 6DNA · UniProt P17174

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