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Amppcp-bound structure of human platelet phosphofructokinase in an R- state, crystal form II

Analyse Amppcp-bound structure of human platelet phosphofructokinase in an R- state… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4RH3
Type: protein
Length: 2,924 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP-dependent 6-phosphofructokinase, platelet type
EC: 2.7.1.11
UniProt: Q01813
Ligands: ACP, PO4
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 47% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	ATP-dependent 6-phosphofructokinase, platelet type (EC 2.7.1.11)	protein	731	47% helix, 18% strand	Q01813

Ligands and binding sites

ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 4 copies · chains A, B, C, D
PO4 · Phosphate ion · ion · 7 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	918	0.82	0.84	82	empty
2	641	0.81	0.86	68	empty
3	655	0.81	0.85	52	empty
4	657	0.80	0.84	51	empty
5	737	0.80	0.83	64	empty

Interfaces

4 interfaces between chains.

A–B · 2455 Å² buried · 35 hydrogen bonds · protein-protein
C–D · 2333 Å² buried · 32 hydrogen bonds · protein-protein
B–C · 777 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 767 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

4RH3 · AMPPCP-bound structure of human platelet phosphofructokinase in an R-state, crystal form… · the same entry in another collection · chain A against A, TM-score 1.00
Q01813 · AlphaFold monomer V2.0 prediction for ATP-dependent 6-phosphofructokinase, platelet type… · a predicted model of the same protein · 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 Q01813
Elsewhere: RCSB PDB 4RH3 · PDBe 4RH3 · UniProt Q01813

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