MolNFT v1 · #137777 · protein
Crystal structure of lactococcus lactis pyruvate carboxylase G746A mutant in complex with cyclic-di-AMP
5VZ0: “Crystal structure of lactococcus lactis pyruvate carboxylase G746A mutant in complex with cyclic-di-AMP”. X-ray diffraction, 4 ligands (ADP, 2BA, MN), 20 pockets (best druggability 0.85). MolNFT v1 #137777 on GenesisL1: 3D…
- PDB
- 5VZ0
- Type
- protein
- Length
- 4,488 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate carboxylase
- EC
- 6.4.1.1
- UniProt
- A0A089XIW4
- Ligands
- ADP, 2BA, MN, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate carboxylase (EC 6.4.1.1) | protein | 1139 | 40% helix, 21% strand | A0A089XIW4 |
| B | Pyruvate carboxylase (EC 6.4.1.1) | protein | 1138 | 40% helix, 21% strand | A0A089XIW4 |
| C | Pyruvate carboxylase (EC 6.4.1.1) | protein | 1074 | 40% helix, 21% strand | A0A089XIW4 |
| D | Pyruvate carboxylase (EC 6.4.1.1) | protein | 1137 | 41% helix, 21% strand | A0A089XIW4 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, B, D
- 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, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 3 copies · chains A, B, 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 | 1032 | 0.85 | 0.86 | 132 | empty |
| 2 | 1157 | 0.85 | 0.86 | 131 | empty |
| 3 | 482 | 0.81 | 0.88 | 75 | empty |
| 4 | 442 | 0.81 | 0.88 | 72 | empty |
| 5 | 1039 | 0.77 | 0.79 | 83 | ADP, MG |
Interfaces
6 interfaces between chains.
- A–C · 2368 Ų buried · 53 hydrogen bonds · protein-protein
- B–D · 2351 Ų buried · 50 hydrogen bonds · protein-protein
- B–C · 1808 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1754 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1750 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5VZ0 · Crystal structure of Lactococcus lactis pyruvate carboxylase G746A mutant in complex with… · 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 A0A089XIW4
- Elsewhere: RCSB PDB 5VZ0 · PDBe 5VZ0 · UniProt A0A089XIW4
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