Research workbench
Structure of a metallo-B-lactamase
Analyse Structure of a metallo-B-lactamase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WYM
- Type
- protein
- Length
- 1,802 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-ascorbate-6-phosphate lactonase ulag
- EC
- 3.1.1.-
- UniProt
- P39300
- Ligands
- MN
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 26% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-ascorbate-6-phosphate lactonase ulag (EC 3.1.1.-) | protein | 303 | 26% helix, 23% strand | P39300 |
| B | L-ascorbate-6-phosphate lactonase ulag (EC 3.1.1.-) | protein | 300 | 26% helix, 23% strand | P39300 |
| C | L-ascorbate-6-phosphate lactonase ulag (EC 3.1.1.-) | protein | 298 | 25% helix, 22% strand | P39300 |
| D | L-ascorbate-6-phosphate lactonase ulag (EC 3.1.1.-) | protein | 300 | 29% helix, 24% strand | P39300 |
| E | L-ascorbate-6-phosphate lactonase ulag (EC 3.1.1.-) | protein | 300 | 27% helix, 24% strand | P39300 |
| F | L-ascorbate-6-phosphate lactonase ulag (EC 3.1.1.-) | protein | 301 | 24% helix, 23% strand | P39300 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 7 copies · chains A, D, B, C, E, F
- FLC · Citrate anion · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 573 | 0.87 | 0.92 | 47 | GOL |
| 2 | 612 | 0.87 | 0.92 | 46 | empty |
| 3 | 594 | 0.86 | 0.92 | 47 | GOL |
| 4 | 159 | 0.51 | 0.79 | 23 | empty |
| 5 | 160 | 0.50 | 0.78 | 24 | empty |
Interfaces
12 interfaces between chains.
- A–F · 3288 Ų buried · 48 hydrogen bonds · protein-protein
- B–E · 3152 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 3114 Ų buried · 43 hydrogen bonds · protein-protein
- A–E · 1296 Ų buried · 32 hydrogen bonds · protein-protein
- D–F · 1273 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (formylation).
Compared structures
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 P39300
- Elsewhere: RCSB PDB 2WYM · PDBe 2WYM · UniProt P39300
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