MolNFT v1 · #105030 · protein
Crystal structure of L. monocytogenes pyruvate carboxylase in complex with cyclic-di-AMP
4QSK: “Crystal structure of L. monocytogenes pyruvate carboxylase in complex with cyclic-di-AMP”. X-ray diffraction, 2 ligands (2BA, MN), 20 pockets (best druggability 0.82). MolNFT v1 #105030 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4QSK
- Type
- protein
- Length
- 2,146 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate carboxylase
- EC
- 6.4.1.1
- UniProt
- W6G6F5
- Ligands
- 2BA, MN
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pyruvate carboxylase (EC 6.4.1.1) | protein | 1073 | 39% helix, 20% strand | W6G6F5 |
Ligands and binding sites
- 2BA · (2r,3r,3as,5r,7ar,9r,10r,10as,12r,14ar)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-D:3', 2'-J][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5, 10,12-tetrol 5,12-dioxide · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- FLC · Citrate anion · additive · 2 copies · chains A, 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 252 | 0.82 | 0.94 | 46 | empty |
| 2 | 232 | 0.79 | 0.92 | 37 | empty |
| 3 | 775 | 0.77 | 0.81 | 59 | FLC |
| 4 | 634 | 0.76 | 0.82 | 55 | FLC |
| 5 | 364 | 0.73 | 0.85 | 43 | empty |
Interfaces
1 interface between chains.
- A–B · 3400 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 4QSK · Crystal Structure of L. monocytogenes Pyruvate Carboxylase in complex with Cyclic-di-AMP · the same entry in another collection · 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 W6G6F5
- Elsewhere: RCSB PDB 4QSK · PDBe 4QSK · UniProt W6G6F5
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