MolNFT v1 · #79357 · protein

Crystal structure of S. aureus pyruvate kinase

3T0T: “Crystal structure of S. aureus pyruvate kinase”. X-ray diffraction, 2 ligands (I30, PO4), 20 pockets (best druggability 0.77). MolNFT v1 #79357 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3T0T
Type: protein
Length: 2,332 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyruvate kinase
EC: 2.7.1.40
UniProt: Q6GG09
Ligands: I30, PO4
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Pyruvate kinase (EC 2.7.1.40)	protein	583	34% helix, 23% strand	Q6GG09

Ligands and binding sites

I30 · N'-[(1E)-1-(1H-benzimidazol-2-yl)ethylidene]-5-bromo-2-hydroxybenzohydrazide · ligand · 2 copies · chains A, B, C, D
PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, 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	1076	0.77	0.79	83	empty
2	994	0.77	0.79	82	empty
3	769	0.77	0.81	37	empty
4	1064	0.77	0.79	85	empty
5	1020	0.76	0.79	84	empty

Interfaces

4 interfaces between chains.

A–B · 1984 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 1982 Å² buried · 25 hydrogen bonds · protein-protein
B–C · 1285 Å² buried · 21 hydrogen bonds · protein-protein
A–D · 1284 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

3T0T · Crystal structure of S. aureus Pyruvate Kinase · the same entry in another collection · chain A against A, TM-score 1.00
Q6GG09 · AlphaFold monomer V2.0 prediction for pyruvate kinase (Q6GG09) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q6GG09
Elsewhere: RCSB PDB 3T0T · PDBe 3T0T · UniProt Q6GG09

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