MolNFT v1 · #49259 · protein
Stenotrophomonas maltophilia L1 metallo-beta-lactamase asp-120 cys mutant
2QIN · Metallo-beta-lactamase L1: “Stenotrophomonas maltophilia L1 metallo-beta-lactamase asp-120 cys mutant”. X-ray diffraction, 2 ligands (ZN, MG), 13 pockets (best druggability 0.88). MolNFT v1 #49259 on GenesisL1: 3D structure, binding…
- PDB
- 2QIN
- Type
- protein
- Length
- 1,057 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallo-beta-lactamase L1
- EC
- 3.5.2.6
- UniProt
- P52700
- Ligands
- ZN, MG
- Pockets
- 13 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metallo-beta-lactamase L1 (EC 3.5.2.6) | protein | 263 | 31% helix, 24% strand | P52700 |
| B | Metallo-beta-lactamase L1 (EC 3.5.2.6) | protein | 264 | 30% helix, 23% strand | P52700 |
| C, D | Metallo-beta-lactamase L1 (EC 3.5.2.6) | protein | 265 | 31% helix, 23% strand | P52700 |
Ligands and binding sites
- ZN · Zinc ion · metal · 9 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1131 | 0.88 | 0.89 | 102 | empty |
| 2 | 498 | 0.79 | 0.86 | 38 | empty |
| 3 | 463 | 0.77 | 0.85 | 37 | empty |
| 4 | 221 | 0.66 | 0.84 | 36 | empty |
| 5 | 268 | 0.65 | 0.82 | 36 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1279 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1256 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 765 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 726 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 476 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2QIN · Stenotrophomonas maltophilia L1 Metallo-beta-Lactamase Asp-120 Cys mutant · the same entry in another collection · chain D against D, TM-score 1.00
- P52700 · AlphaFold monomer V2.0 prediction for metallo-beta-lactamase L1 type 3 (P52700) · a predicted model of the same protein · chain D 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 P52700
- Elsewhere: RCSB PDB 2QIN · PDBe 2QIN · UniProt P52700
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