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The structure of trans-3-chloroacrylic acid dehalogenase, covalently inactivated by the mechanism-based inhibitor 3-bromopropiolate at 2.3 ångström resolution
Analyse The structure of trans-3-chloroacrylic acid dehalogenase, covalently… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1S0Y
- Type
- protein
- Length
- 702 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-subunit of trans-3-chloroacrylic acid dehalogenase; Beta-subunit of…
- UniProt
- Q9EV85, Q9EV84
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 42% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G, I | Alpha-subunit of trans-3-chloroacrylic acid dehalogenase | protein | 62 | 40% helix, 31% strand | Q9EV85 |
| B, J, L | Beta-subunit of trans-3-chloroacrylic acid dehalogenase | protein | 55 | 45% helix, 29% strand | Q9EV84 |
| C | Alpha-subunit of trans-3-chloroacrylic acid dehalogenase | protein | 60 | 42% helix, 32% strand | Q9EV85 |
| D, H | Beta-subunit of trans-3-chloroacrylic acid dehalogenase | protein | 56 | 45% helix, 29% strand | Q9EV84 |
| E, K | Alpha-subunit of trans-3-chloroacrylic acid dehalogenase | protein | 61 | 41% helix, 31% strand | Q9EV85 |
| F | Beta-subunit of trans-3-chloroacrylic acid dehalogenase | protein | 57 | 42% helix, 28% strand | Q9EV84 |
Ligands and binding sites
- MLA · Malonic acid · additive · 6 copies · chains B, C, E, A, D, F, H, I, K, G, J, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 544 | 0.76 | 0.83 | 94 | empty |
| 2 | 154 | 0.51 | 0.79 | 33 | empty |
| 3 | 141 | 0.50 | 0.79 | 26 | empty |
| 4 | 108 | 0.43 | 0.78 | 21 | empty |
| 5 | 133 | 0.42 | 0.76 | 26 | empty |
Interfaces
36 interfaces between chains.
- A–D · 1119 Ų buried · 11 hydrogen bonds · protein-protein
- H–K · 1107 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 1095 Ų buried · 12 hydrogen bonds · protein-protein
- C–F · 1084 Ų buried · 13 hydrogen bonds · protein-protein
- I–L · 1031 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (additive adduct).
Compared structures
- 1S0Y · The structure of trans-3-chloroacrylic acid dehalogenase, covalently inactivated by the… · 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 Q9EV85
- Every structure of UniProt Q9EV84
- Elsewhere: RCSB PDB 1S0Y · PDBe 1S0Y · UniProt Q9EV85 · UniProt Q9EV84
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