Research workbench
Crystal structure of the metallo-beta-lactamase L1 from stenotrophomonas maltophilia
Analyse Crystal structure of the metallo-beta-lactamase L1 from stenotrophomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U0Y
- Type
- protein
- Length
- 1,061 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative metallo-beta-lactamase L1 (beta-lactamase type II) (ec 3.5.2.6) (penicillinase)
- EC
- 3.5.2.6
- UniProt
- B2FTM1
- Ligands
- ZN
- Pockets
- 13 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative metallo-beta-lactamase L1 (beta-lactamase type II) (ec 3.5.2.6) (penicillinase) (EC 3.5.2.6) | protein | 265 | 31% helix, 24% strand | B2FTM1 |
| B, D | Putative metallo-beta-lactamase L1 (beta-lactamase type II) (ec 3.5.2.6) (penicillinase) (EC 3.5.2.6) | protein | 266 | 31% helix, 24% strand | B2FTM1 |
| C | Putative metallo-beta-lactamase L1 (beta-lactamase type II) (ec 3.5.2.6) (penicillinase) (EC 3.5.2.6) | protein | 264 | 31% helix, 24% strand | B2FTM1 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, C, 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1021 | 0.86 | 0.87 | 93 | EDO |
| 2 | 439 | 0.80 | 0.88 | 34 | empty |
| 3 | 442 | 0.79 | 0.87 | 40 | empty |
| 4 | 280 | 0.66 | 0.83 | 39 | empty |
| 5 | 292 | 0.65 | 0.81 | 42 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1338 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1300 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 733 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 730 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 420 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6U0Y · Crystal Structure of the metallo-beta-lactamase L1 from Stenotrophomonas maltophilia · 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 B2FTM1
- Elsewhere: RCSB PDB 6U0Y · PDBe 6U0Y · UniProt B2FTM1
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