Research workbench
Crystal structure of oxa-163 complexed with iodide in the active site
Analyse Crystal structure of oxa-163 complexed with iodide in the active site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4S2M
- Type
- protein
- Length
- 934 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- F6KZJ2
- Ligands
- IOD
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 232 | 38% helix, 19% strand | F6KZJ2 |
| B, C | Beta-lactamase (EC 3.5.2.6) | protein | 234 | 40% helix, 19% strand | F6KZJ2 |
| D | Beta-lactamase (EC 3.5.2.6) | protein | 234 | 38% helix, 19% strand | F6KZJ2 |
Ligands and binding sites
- IOD · Iodide ion · ion · 20 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 580 | 0.77 | 0.84 | 91 | IOD |
| 2 | 538 | 0.76 | 0.84 | 92 | IOD |
| 3 | 1112 | 0.76 | 0.79 | 91 | IOD |
| 4 | 94 | 0.44 | 0.79 | 17 | empty |
| 5 | 63 | 0.40 | 0.80 | 18 | empty |
Interfaces
5 interfaces between chains.
- B–C · 917 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 917 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 194 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 190 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 65 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4S2M · Crystal Structure of OXA-163 complexed with iodide in the active site · 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 F6KZJ2
- Elsewhere: RCSB PDB 4S2M · PDBe 4S2M · UniProt F6KZJ2
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