MolNFT v1 · #105027 · protein
Crystal structure of L. monocytogenes pyruvate carboxylase in complex with cyclic-di-AMP
4QSH: “Crystal structure of L. monocytogenes pyruvate carboxylase in complex with cyclic-di-AMP”. X-ray diffraction, 2 ligands (2BA, MN), 20 pockets (best druggability 0.83). MolNFT v1 #105027 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4QSH
- Type
- protein
- Length
- 4,299 residues
- Chains
- 4
- 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 0.83
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate carboxylase (EC 6.4.1.1) | protein | 1072 | 39% helix, 20% strand | W6G6F5 |
| B | Pyruvate carboxylase (EC 6.4.1.1) | protein | 1074 | 39% helix, 20% strand | W6G6F5 |
| C | Pyruvate carboxylase (EC 6.4.1.1) | protein | 1081 | 39% helix, 20% strand | W6G6F5 |
| D | Pyruvate carboxylase (EC 6.4.1.1) | protein | 1072 | 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 · 3 copies · chains A, D, B, C
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- FLC · Citrate anion · additive · 4 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1068 | 0.83 | 0.84 | 119 | MN |
| 2 | 795 | 0.82 | 0.85 | 83 | empty |
| 3 | 229 | 0.81 | 0.94 | 38 | empty |
| 4 | 221 | 0.81 | 0.94 | 39 | empty |
| 5 | 897 | 0.79 | 0.82 | 89 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3418 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 3416 Ų buried · 48 hydrogen bonds · protein-protein
- A–D · 1630 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1600 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1110 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4QSH · 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 4QSH · PDBe 4QSH · UniProt W6G6F5
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