MolNFT v1 · #122486 · protein
RM3 metallo-beta-lactamase
5IQK · Beta-lactamase RM3: “RM3 metallo-beta-lactamase”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.84). MolNFT v1 #122486 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5IQK
- Type
- protein
- Length
- 539 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase RM3
- EC
- 3.5.2.6
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase RM3 (EC 3.5.2.6) | protein | 269 | 36% helix, 22% strand | — |
| B | Beta-lactamase RM3 (EC 3.5.2.6) | protein | 270 | 36% helix, 21% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1099 | 0.84 | 0.85 | 105 | ZN |
| 2 | 63 | 0.38 | 0.79 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1171 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5IQK · Rm3 metallo-beta-lactamase · 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
- Elsewhere: RCSB PDB 5IQK · PDBe 5IQK
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