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Crystal structure of the bacillus stearothermophilus phosphofructokinase mutant D12A in complex with pep

Analyse Crystal structure of the bacillus stearothermophilus phosphofructokinase mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4I7E
Type: protein
Length: 1,276 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 6-phosphofructokinase
EC: 2.7.1.11
UniProt: P00512
Ligands: PEP
Pockets: 15 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	6-phosphofructokinase (EC 2.7.1.11)	protein	319	44% helix, 20% strand	P00512

Ligands and binding sites

PEP · Phosphoenolpyruvate · ligand · 4 copies · chains A, B, C, D

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

Pockets

15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1200	0.84	0.86	83	empty
2	200	0.83	0.96	30	empty
3	156	0.80	0.95	28	empty
4	705	0.72	0.79	71	PEP
5	686	0.70	0.78	66	PEP

Interfaces

6 interfaces between chains.

C–D · 2297 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 2277 Å² buried · 25 hydrogen bonds · protein-protein
A–D · 1258 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 1163 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 87 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4I7E · Crystal Structure of the Bacillus stearothermophilus Phosphofructokinase Mutant D12A in… · the same entry in another collection · chain A against A, TM-score 1.00
P00512 · AlphaFold monomer V2.0 prediction for ATP-dependent 6-phosphofructokinase (P00512) · a predicted model of the same protein · chain A 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 P00512
Elsewhere: RCSB PDB 4I7E · PDBe 4I7E · UniProt P00512

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