MolNFT v1 · #172318 · protein
Structure of ndm-1 with 2-mercaptomethyl-thiazolidine L-anti-1B
6ZYP · Metallo-beta-lactamase type 2: “Structure of ndm-1 with 2-mercaptomethyl-thiazolidine L-anti-1B”. X-ray diffraction, 3 ligands (QT2, ZN, SO4), 4 pockets (best druggability 0.78). MolNFT v1 #172318 on GenesisL1: 3D structure, binding…
- PDB
- 6ZYP
- Type
- protein
- Length
- 469 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallo-beta-lactamase type 2
- EC
- 3.5.2.6
- UniProt
- C7C422
- Ligands
- QT2, ZN, SO4
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metallo-beta-lactamase type 2 (EC 3.5.2.6) | protein | 241 | 24% helix, 29% strand | C7C422 |
| B | Metallo-beta-lactamase type 2 (EC 3.5.2.6) | protein | 228 | 24% helix, 30% strand | C7C422 |
Ligands and binding sites
- QT2 · (2~{S},4~{R})-2-ethoxycarbonyl-5,5-dimethyl-2-(sulfanylmethyl)-1,3-thiazolidine-4-carboxylic acid · ligand · chains A
- ZN · Zinc ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.78 | 0.97 | 22 | empty |
| 2 | 125 | 0.60 | 0.86 | 32 | empty |
| 3 | 237 | 0.51 | 0.76 | 33 | QT2 |
| 4 | 167 | 0.47 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 905 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6ZYP · Structure of NDM-1 with 2-Mercaptomethyl-thiazolidine L-anti-1b · the same entry in another collection · chain A against A, TM-score 1.00
- C7C422 · AlphaFold monomer V2.0 prediction for metallo-beta-lactamase type 2 (C7C422) · a predicted model of the same protein · chain B 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 C7C422
- Elsewhere: RCSB PDB 6ZYP · PDBe 6ZYP · UniProt C7C422
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