MolNFT v1 · #135718 · protein
Crystal structure of a the tin-bound form of merb formed from diethyltin.
5U7B · Alkylmercury lyase: “Crystal structure of a the tin-bound form of merb formed from diethyltin.”. X-ray diffraction, 2 ligands (ZN6, BR), 5 pockets (best druggability 0.82). MolNFT v1 #135718 on GenesisL1: 3D structure, binding sites…
- PDB
- 5U7B
- Type
- protein
- Length
- 416 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alkylmercury lyase
- EC
- 4.99.1.2
- UniProt
- P77072
- Ligands
- ZN6, BR
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alkylmercury lyase (EC 4.99.1.2) | protein | 208 | 42% helix, 22% strand | P77072 |
Ligands and binding sites
- ZN6 · Diethyltin dichloride · metal · 2 copies · chains A, B
- BR · Bromide ion · ion · chains A
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 278 | 0.82 | 0.93 | 38 | empty |
| 2 | 203 | 0.81 | 0.95 | 30 | empty |
| 3 | 981 | 0.81 | 0.83 | 67 | ACT |
| 4 | 80 | 0.40 | 0.78 | 15 | empty |
| 5 | 102 | 0.38 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 869 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5U7B · Crystal structure of a the tin-bound form of MerB formed from Diethyltin. · the same entry in another collection · chain A against A, TM-score 1.00
- P77072 · AlphaFold monomer V2.0 prediction for alkylmercury lyase (P77072) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P77072
- Elsewhere: RCSB PDB 5U7B · PDBe 5U7B · UniProt P77072
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