MolNFT v1 · #49297 · protein
Stenotrophomonas maltophilia L1 metallo-beta-lactamase asp-120 asn mutant
2QJS · Metallo-beta-lactamase L1: “Stenotrophomonas maltophilia L1 metallo-beta-lactamase asp-120 asn mutant”. X-ray diffraction, 1 ligand (ZN), 8 pockets (best druggability 0.88). MolNFT v1 #49297 on GenesisL1: 3D structure, binding sites…
- PDB
- 2QJS
- Type
- protein
- Length
- 992 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
- Pockets
- 8 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Metallo-beta-lactamase L1 (EC 3.5.2.6) | protein | 248 | 30% helix, 22% strand | P52700 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 903 | 0.88 | 0.90 | 99 | empty |
| 2 | 481 | 0.81 | 0.88 | 37 | empty |
| 3 | 496 | 0.81 | 0.88 | 41 | empty |
| 4 | 583 | 0.67 | 0.77 | 52 | empty |
| 5 | 136 | 0.46 | 0.77 | 29 | ZN |
Interfaces
6 interfaces between chains.
- B–D · 826 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 822 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 416 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 403 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 366 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2QJS · Stenotrophomonas maltophilia L1 metallo-beta-lactamase Asp-120 Asn 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 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 P52700
- Elsewhere: RCSB PDB 2QJS · PDBe 2QJS · UniProt P52700
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