Research workbench
Crystal structure of the lead-bound form of merb formed from diethyllead.
Analyse Crystal structure of the lead-bound form of merb formed from diethyllead. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U7C
- 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
- ZN7, BR
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alkylmercury lyase (EC 4.99.1.2) | protein | 208 | 41% helix, 22% strand | P77072 |
Ligands and binding sites
- ZN7 · Diethyllead dibromide · 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 | 231 | 0.81 | 0.94 | 31 | empty |
| 2 | 1036 | 0.81 | 0.83 | 83 | ACT |
| 3 | 252 | 0.81 | 0.93 | 35 | empty |
| 4 | 121 | 0.43 | 0.77 | 15 | empty |
| 5 | 138 | 0.42 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 909 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5U7C · Crystal structure of the lead-bound form of MerB formed from diethyllead. · 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 0.99
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 P77072
- Elsewhere: RCSB PDB 5U7C · PDBe 5U7C · UniProt P77072
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