MolNFT v1 · #140882 · protein
Crystal structure of ndm-1 bound to hydrolyzed imipenem representing an EI1 complex
5YPI · Metallo-beta-lactamase ndm-1: “Crystal structure of ndm-1 bound to hydrolyzed imipenem representing an EI1 complex”. X-ray diffraction, 4 ligands (8YF, ZN, SO4), 20 pockets (best druggability 0.81). MolNFT v1 #140882 on GenesisL1…
- PDB
- 5YPI
- Type
- protein
- Length
- 1,824 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallo-beta-lactamase ndm-1
- UniProt
- A0A0A7Y424
- Ligands
- 8YF, ZN, SO4, CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Metallo-beta-lactamase ndm-1 | protein | 228 | 24% helix, 33% strand | A0A0A7Y424 |
Ligands and binding sites
- 8YF · (2R)-2-[(2S,3R)-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-(2-methanimidamidoethylsulfanyl)-2,3-dihydro-1H-pyrrole-5-carboxylic acid · ligand · 8 copies · chains A, E, B, C, D, F, G, H
- ZN · Zinc ion · metal · 16 copies · chains A, B, C, D, E, F, G, H
- SO4 · Sulfate ion · ion · 7 copies · chains A, H, B, C, E, D, G
- CL · Chloride ion · ion · chains C
- GOL · Glycerol · additive · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 986 | 0.81 | 0.83 | 95 | ZN, 8YF, SO4 |
| 2 | 108 | 0.78 | 0.98 | 21 | empty |
| 3 | 105 | 0.78 | 0.97 | 21 | empty |
| 4 | 844 | 0.73 | 0.78 | 106 | empty |
| 5 | 920 | 0.69 | 0.74 | 82 | SO4 |
Interfaces
15 interfaces between chains.
- D–G · 974 Ų buried · 7 hydrogen bonds · protein-protein
- B–F · 955 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 564 Ų buried · 4 hydrogen bonds · protein-protein
- C–H · 388 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 318 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5YPI · Crystal structure of NDM-1 bound to hydrolyzed imipenem representing an EI1 complex · 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 A0A0A7Y424
- Elsewhere: RCSB PDB 5YPI · PDBe 5YPI · UniProt A0A0A7Y424
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