Research workbench
Crystal structure of beta-alanine synthase from saccharomyces kluyveri in complex with a gly-gly peptide
Analyse Crystal structure of beta-alanine synthase from saccharomyces kluyveri in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VL1
- Type
- protein
- Length
- 1,744 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-alanine synthase
- EC
- 3.5.1.6
- UniProt
- Q96W94
- Ligands
- ZN
- Pockets
- 15 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-alanine synthase (EC 3.5.1.6) | protein | 435 | 36% helix, 22% strand | Q96W94 |
| B, D | Beta-alanine synthase (EC 3.5.1.6) | protein | 436 | 36% helix, 22% strand | Q96W94 |
| C | Beta-alanine synthase (EC 3.5.1.6) | protein | 437 | 36% helix, 22% strand | Q96W94 |
Ligands and binding sites
- ZN · Zinc ion · metal · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1010 | 0.77 | 0.79 | 91 | empty |
| 2 | 276 | 0.56 | 0.77 | 28 | empty |
| 3 | 153 | 0.52 | 0.80 | 23 | empty |
| 4 | 145 | 0.51 | 0.79 | 23 | empty |
| 5 | 88 | 0.50 | 0.83 | 22 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2842 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 2824 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 195 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 156 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 101 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2VL1 · Crystal structure of beta-alanine synthase from Saccharomyces kluyveri in complex with a… · 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 Q96W94
- Elsewhere: RCSB PDB 2VL1 · PDBe 2VL1 · UniProt Q96W94
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