Research workbench
Wild-type hydroxycinnamoyl-CoA hydratase lyase in complex with acetyl- CoA and vanillin
Analyse Wild-type hydroxycinnamoyl-CoA hydratase lyase in complex with acetyl- CoA and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VSS
- Type
- protein
- Length
- 1,452 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- P-hydroxycinnamoyl CoA HYDRATASE/LYASE
- EC
- 4.2.1.101
- UniProt
- O69762
- Ligands
- ACO, V55
- Pockets
- 19 · best druggability 0.88
Structure
x-ray diffraction · 6 distinct chains · 51% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | P-hydroxycinnamoyl CoA HYDRATASE/LYASE (EC 4.2.1.101) | protein | 238 | 51% helix, 18% strand | O69762 |
| B | P-hydroxycinnamoyl CoA HYDRATASE/LYASE (EC 4.2.1.101) | protein | 247 | 51% helix, 19% strand | O69762 |
| C | P-hydroxycinnamoyl CoA HYDRATASE/LYASE (EC 4.2.1.101) | protein | 235 | 50% helix, 18% strand | O69762 |
| D | P-hydroxycinnamoyl CoA HYDRATASE/LYASE (EC 4.2.1.101) | protein | 246 | 52% helix, 18% strand | O69762 |
| E | P-hydroxycinnamoyl CoA HYDRATASE/LYASE (EC 4.2.1.101) | protein | 240 | 51% helix, 19% strand | O69762 |
| F | P-hydroxycinnamoyl CoA HYDRATASE/LYASE (EC 4.2.1.101) | protein | 246 | 53% helix, 18% strand | O69762 |
Ligands and binding sites
- ACO · Acetyl coenzyme *A · ligand · 4 copies · chains B, D, E, F
- V55 · 4-hydroxy-3-methoxybenzaldehyde · ligand · chains D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 636 | 0.88 | 0.93 | 61 | empty |
| 2 | 591 | 0.88 | 0.93 | 65 | empty |
| 3 | 564 | 0.88 | 0.94 | 60 | empty |
| 4 | 989 | 0.88 | 0.90 | 103 | empty |
| 5 | 391 | 0.71 | 0.82 | 44 | ACO |
Interfaces
15 interfaces between chains.
- B–C · 1711 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1708 Ų buried · 23 hydrogen bonds · protein-protein
- D–F · 1698 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1688 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1682 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 2VSS · Wild-type Hydroxycinnamoyl-CoA hydratase lyase in complex with acetyl- CoA and vanillin · the same entry in another collection · chain F against F, TM-score 1.00
- O69762 · AlphaFold monomer V2.0 prediction for hydroxycinnamoyl-CoA hydratase- lyase (O69762) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 O69762
- Elsewhere: RCSB PDB 2VSS · PDBe 2VSS · UniProt O69762
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