Research workbench
Directed evolutionary changes in mbl super family - vim-2 round 10
Analyse Directed evolutionary changes in mbl super family - vim-2 round 10 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BM9
- Type
- protein
- Length
- 902 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallo-beta-lactamase
- UniProt
- Q5U7L7
- Ligands
- ZN
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metallo-beta-lactamase | protein | 228 | 24% helix, 26% strand | Q5U7L7 |
| B | Metallo-beta-lactamase | protein | 225 | 25% helix, 26% strand | Q5U7L7 |
| C | Metallo-beta-lactamase | protein | 224 | 25% helix, 29% strand | Q5U7L7 |
| D | Metallo-beta-lactamase | protein | 225 | 25% helix, 27% strand | Q5U7L7 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.79 | 0.98 | 30 | empty |
| 2 | 191 | 0.78 | 0.94 | 36 | empty |
| 3 | 186 | 0.78 | 0.94 | 37 | empty |
| 4 | 218 | 0.76 | 0.91 | 48 | ZN |
| 5 | 50 | 0.61 | 0.93 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 3537 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 3467 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 6BM9 · Directed evolutionary changes in MBL super family - VIM-2 Round 10 · 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 Q5U7L7
- Elsewhere: RCSB PDB 6BM9 · PDBe 6BM9 · UniProt Q5U7L7
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