MolNFT v1 · #95307 · protein
The structure of C436M-hlpyk in complex with CITRATE/MN/ATP/FRU-1,6-bp
4IMA · Pyruvate kinase: “The structure of C436M-hlpyk in complex with CITRATE/MN/ATP/FRU-1,6-bp”. X-ray diffraction, 3 ligands (FBP, ADN, MN), 20 pockets (best druggability 0.86). MolNFT v1 #95307 on GenesisL1: 3D structure, binding sites…
- PDB
- 4IMA
- Type
- protein
- Length
- 1,987 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate kinase
- EC
- 2.7.1.40
- UniProt
- O75758
- Ligands
- FBP, ADN, MN
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate kinase (EC 2.7.1.40) | protein | 522 | 41% helix, 22% strand | O75758 |
| B | Pyruvate kinase (EC 2.7.1.40) | protein | 500 | 41% helix, 19% strand | O75758 |
| C | Pyruvate kinase (EC 2.7.1.40) | protein | 505 | 40% helix, 20% strand | O75758 |
| D | Pyruvate kinase (EC 2.7.1.40) | protein | 460 | 46% helix, 16% strand | O75758 |
Ligands and binding sites
- FBP · 1,6-di-O-phosphono-beta-D-fructofuranose · ligand · 4 copies · chains A, B, C, D
- ADN · Adenosine · ligand · chains D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- FLC · Citrate anion · additive · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · chains B
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 333 | 0.86 | 0.96 | 45 | empty |
| 2 | 342 | 0.86 | 0.95 | 46 | empty |
| 3 | 721 | 0.83 | 0.87 | 53 | empty |
| 4 | 536 | 0.78 | 0.85 | 59 | MN, FLC |
| 5 | 997 | 0.77 | 0.79 | 112 | MN, FLC |
Interfaces
6 interfaces between chains.
- A–C · 2836 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 2811 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 1698 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1631 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 40 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4IMA · The structure of C436M-hLPYK in complex with Citrate/Mn/ATP/Fru-1,6-BP · the same entry in another collection · chain B against B, 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 O75758
- Elsewhere: RCSB PDB 4IMA · PDBe 4IMA · UniProt O75758
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.