MolNFT v1 · #140884 · protein
Crystal structure of ndm-1 bound to hydrolyzed imipenem representing an EI2 complex
5YPK · Metallo-beta-lactamase ndm-1: “Crystal structure of ndm-1 bound to hydrolyzed imipenem representing an EI2 complex”. X-ray diffraction, 5 ligands (HIW, ZN, NA), 20 pockets (best druggability 0.81). MolNFT v1 #140884 on GenesisL1: 3D…
- PDB
- 5YPK
- Type
- protein
- Length
- 1,826 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallo-beta-lactamase ndm-1
- UniProt
- A0A0A7Y424
- Ligands
- HIW, ZN, NA, SO4, CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F, H | Metallo-beta-lactamase ndm-1 | protein | 228 | 23% helix, 32% strand | A0A0A7Y424 |
| D, G | Metallo-beta-lactamase ndm-1 | protein | 229 | 23% helix, 33% strand | A0A0A7Y424 |
Ligands and binding sites
- HIW · (2R,4S)-2-[(1S,2R)-1-carboxy-2-hydroxypropyl]-4-[(2-{[(Z)-iminomethyl]amino}ethyl)sulfanyl]-3,4-dihydro-2H-pyrrole-5-carboxylic acid · ligand · 8 copies · chains A, H, B, C, D, E, F, G
- ZN · Zinc ion · metal · 16 copies · chains A, B, C, D, E, F, G, H
- NA · Sodium ion · metal · 7 copies · chains C, E, D, F, B, G
- SO4 · Sulfate ion · ion · 7 copies · chains A, E, B, C, H, D, F
- CL · Chloride ion · ion · chains D, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 928 | 0.81 | 0.83 | 93 | HIW, ZN |
| 2 | 105 | 0.79 | 0.98 | 21 | empty |
| 3 | 114 | 0.79 | 0.98 | 20 | empty |
| 4 | 766 | 0.71 | 0.77 | 105 | empty |
| 5 | 444 | 0.64 | 0.77 | 44 | SO4 |
Interfaces
15 interfaces between chains.
- B–G · 975 Ų buried · 5 hydrogen bonds · protein-protein
- D–F · 957 Ų buried · 6 hydrogen bonds · protein-protein
- A–H · 615 Ų buried · 4 hydrogen bonds · protein-protein
- C–E · 467 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 300 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5YPK · Crystal structure of NDM-1 bound to hydrolyzed imipenem 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 5YPK · PDBe 5YPK · UniProt A0A0A7Y424
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