Research workbench
Structure of imp-1 with 2-mercaptomethyl-thiazolidine L-anti-1B
Analyse Structure of imp-1 with 2-mercaptomethyl-thiazolidine L-anti-1B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZYR
- Type
- protein
- Length
- 879 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase imp-1
- EC
- 3.5.2.6
- UniProt
- P52699
- Ligands
- QT2, ZN, NA
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Beta-lactamase imp-1 (EC 3.5.2.6) | protein | 219 | 27% helix, 32% strand | P52699 |
| C | Beta-lactamase imp-1 (EC 3.5.2.6) | protein | 222 | 27% helix, 31% strand | P52699 |
Ligands and binding sites
- QT2 · (2~{S},4~{R})-2-ethoxycarbonyl-5,5-dimethyl-2-(sulfanylmethyl)-1,3-thiazolidine-4-carboxylic acid · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- NA · Sodium ion · metal · chains B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
- ACT · Acetate ion · additive · chains 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 483 | 0.77 | 0.85 | 62 | QT2 |
| 2 | 834 | 0.76 | 0.80 | 93 | QT2 |
| 3 | 378 | 0.69 | 0.81 | 41 | QT2 |
| 4 | 232 | 0.55 | 0.77 | 26 | QT2 |
| 5 | 79 | 0.49 | 0.83 | 15 | empty |
Interfaces
4 interfaces between chains.
- A–D · 736 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 534 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 466 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 30 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6ZYR · Structure of IMP-1 with 2-Mercaptomethyl-thiazolidine L-anti-1b · the same entry in another collection · chain D against D, TM-score 1.00
- P52699 · AlphaFold monomer V2.0 prediction for metallo-beta-lactamase type 2 (P52699) · a predicted model of the same protein · 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 P52699
- Elsewhere: RCSB PDB 6ZYR · PDBe 6ZYR · UniProt P52699
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