MolNFT v1 · #140887 · protein
Crystal structure of ndm-1 bound to hydrolyzed meropenem representing an EI2 complex
5YPN · Metallo-beta-lactamase ndm-1: “Crystal structure of ndm-1 bound to hydrolyzed meropenem representing an EI2 complex”. X-ray diffraction, 3 ligands (LMP, ZN, SO4), 3 pockets (best druggability 0.78). MolNFT v1 #140887 on GenesisL1…
- PDB
- 5YPN
- Type
- protein
- Length
- 456 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallo-beta-lactamase ndm-1
- UniProt
- A0A0A7Y424
- Ligands
- LMP, ZN, SO4
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Metallo-beta-lactamase ndm-1 | protein | 228 | 24% helix, 32% strand | A0A0A7Y424 |
Ligands and binding sites
- LMP · (2~{S},3~{R},4~{S})-2-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-[(3~{S},5~{S})-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl-3-methyl-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.78 | 0.98 | 22 | empty |
| 2 | 132 | 0.40 | 0.74 | 24 | ZN, LMP |
| 3 | 102 | 0.35 | 0.73 | 22 | ZN, LMP |
Interfaces
1 interface between chains.
- A–B · 951 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5YPN · Crystal structure of NDM-1 bound to hydrolyzed meropenem representing an EI2 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 5YPN · PDBe 5YPN · UniProt A0A0A7Y424
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