Research workbench
Crystal structure of lactococcus lactis pyruvate carboxylase
Analyse Crystal structure of lactococcus lactis pyruvate carboxylase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VYW
- Type
- protein
- Length
- 3,984 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
- BTN, MN
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate carboxylase (EC 6.4.1.1) | protein | 981 | 44% helix, 18% strand | A0A089XIW4 |
| B | Pyruvate carboxylase (EC 6.4.1.1) | protein | 979 | 44% helix, 18% strand | A0A089XIW4 |
| C | Pyruvate carboxylase (EC 6.4.1.1) | protein | 978 | 44% helix, 18% strand | A0A089XIW4 |
| D | Pyruvate carboxylase (EC 6.4.1.1) | protein | 1046 | 43% helix, 18% strand | A0A089XIW4 |
Ligands and binding sites
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 | 1149 | 0.84 | 0.85 | 117 | empty |
| 2 | 602 | 0.82 | 0.88 | 82 | empty |
| 3 | 1053 | 0.81 | 0.83 | 133 | MN |
| 4 | 383 | 0.78 | 0.88 | 62 | empty |
| 5 | 946 | 0.78 | 0.80 | 108 | MN |
Interfaces
4 interfaces between chains.
- B–C · 3021 Ų buried · 63 hydrogen bonds · protein-protein
- A–D · 2936 Ų buried · 57 hydrogen bonds · protein-protein
- A–C · 1688 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1655 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 5VYW · Crystal structure of Lactococcus lactis pyruvate carboxylase · 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 5VYW · PDBe 5VYW · UniProt A0A089XIW4
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