MolNFT v1 · #94829 · protein

Alanine-glyoxylate aminotransferase variant S187F

4I8A · Serine-pyruvate aminotransferase: “Alanine-glyoxylate aminotransferase variant S187F”. X-ray diffraction, 5 pockets (best druggability 0.79). MolNFT v1 #94829 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4I8A
Type: protein
Length: 1,544 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Serine-pyruvate aminotransferase
EC: 2.6.1.51, 2.6.1.44
UniProt: P21549
Pockets: 5 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 44% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Serine-pyruvate aminotransferase (EC 2.6.1.51, 2.6.1.44)	protein	387	43% helix, 15% strand	P21549
B, D	Serine-pyruvate aminotransferase (EC 2.6.1.51, 2.6.1.44)	protein	386	44% helix, 15% strand	P21549
C	Serine-pyruvate aminotransferase (EC 2.6.1.51, 2.6.1.44)	protein	385	44% helix, 15% strand	P21549

Ligands and binding sites

GOL · Glycerol · additive · 13 copies · chains A, B, C, D

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

Pockets

5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1063	0.79	0.81	127	GOL
2	604	0.73	0.81	66	GOL
3	287	0.66	0.82	38	GOL
4	311	0.62	0.79	37	empty
5	246	0.61	0.80	35	GOL

Interfaces

5 interfaces between chains.

A–B · 4016 Å² buried · 55 hydrogen bonds · protein-protein
C–D · 4006 Å² buried · 55 hydrogen bonds · protein-protein
A–C · 496 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 339 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 41 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (cofactor).

Compared structures

4I8A · Alanine-glyoxylate aminotransferase variant S187F · the same entry in another collection · chain A against A, TM-score 1.00
P21549 · AlphaFold monomer V2.0 prediction for serine--pyruvate aminotransferase (P21549) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 P21549
Elsewhere: RCSB PDB 4I8A · PDBe 4I8A · UniProt P21549

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