MolNFT v1 · #144630 · protein
Crystal structure of halogenase pltm in complex with ethyl mercury and mercury
6BZI: “Crystal structure of halogenase pltm in complex with ethyl mercury and mercury”. X-ray diffraction, 3 ligands (EMC, HG, CA), 20 pockets (best druggability 0.78). MolNFT v1 #144630 on GenesisL1: 3D structure, binding sites and…
- 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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