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Structure of the S12D variant of human liver pyruvate kinase in complex with citrate and fbp.
Analyse Structure of the S12D variant of human liver pyruvate kinase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IP7
- Type
- protein
- Length
- 2,016 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate kinase isozymes L
- EC
- 2.7.1.40
- UniProt
- P30613
- Ligands
- FBP, ADN, MN, NA
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate kinase isozymes L (EC 2.7.1.40) | protein | 506 | 41% helix, 23% strand | P30613 |
| B | Pyruvate kinase isozymes L (EC 2.7.1.40) | protein | 505 | 41% helix, 22% strand | P30613 |
| C | Pyruvate kinase isozymes L (EC 2.7.1.40) | protein | 498 | 41% helix, 22% strand | P30613 |
| D | Pyruvate kinase isozymes L (EC 2.7.1.40) | protein | 507 | 41% helix, 22% strand | P30613 |
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
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, C, D
- FLC · Citrate anion · additive · 4 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 305 | 0.86 | 0.96 | 44 | empty |
| 2 | 297 | 0.85 | 0.95 | 45 | empty |
| 3 | 627 | 0.83 | 0.88 | 51 | empty |
| 4 | 861 | 0.79 | 0.82 | 115 | MN, FLC, NA |
| 5 | 445 | 0.79 | 0.87 | 49 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2857 Ų buried · 37 hydrogen bonds · protein-protein
- B–D · 2837 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 1527 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1496 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 47 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4IP7 · Structure of the S12D variant of human liver pyruvate kinase in complex with citrate and… · the same entry in another collection · chain D against D, 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 P30613
- Elsewhere: RCSB PDB 4IP7 · PDBe 4IP7 · UniProt P30613
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