Research workbench
Crystal structure of halogenase pltm in complex with ethyl mercury and mercury
Analyse Crystal structure of halogenase pltm in complex with ethyl mercury and mercury in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BZI
- Type
- protein
- Length
- 1,971 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Halogenase pltm
- EC
- 3.8.1.1
- UniProt
- Q4KCZ3
- Ligands
- EMC, HG, CA
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Halogenase pltm (EC 3.8.1.1) | protein | 487 | 45% helix, 20% strand | Q4KCZ3 |
| B | Halogenase pltm (EC 3.8.1.1) | protein | 495 | 45% helix, 20% strand | Q4KCZ3 |
| C | Halogenase pltm (EC 3.8.1.1) | protein | 496 | 43% helix, 20% strand | Q4KCZ3 |
| D | Halogenase pltm (EC 3.8.1.1) | protein | 493 | 44% helix, 20% strand | Q4KCZ3 |
Ligands and binding sites
- EMC · Ethyl mercury ion · ligand · 8 copies · chains A, B, C, D
- HG · Mercury (II) ion · metal · 25 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains A, B, C, 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.78 | 0.97 | 32 | empty |
| 2 | 126 | 0.78 | 0.96 | 32 | empty |
| 3 | 523 | 0.76 | 0.83 | 63 | empty |
| 4 | 602 | 0.75 | 0.81 | 60 | empty |
| 5 | 454 | 0.74 | 0.83 | 58 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1284 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1274 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 692 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6BZI · Crystal structure of halogenase PltM in complex with ethyl mercury and mercury · 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 Q4KCZ3
- Elsewhere: RCSB PDB 6BZI · PDBe 6BZI · UniProt Q4KCZ3
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