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Crystal structure of ndm-1 bound to hydrolyzed meropenem representing an EI1 complex
Analyse Crystal structure of ndm-1 bound to hydrolyzed meropenem representing an EI1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YPM
- Type
- protein
- Length
- 1,825 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallo-beta-lactamase ndm-1
- UniProt
- A0A0A7Y424
- Ligands
- 8YL, ZN, SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F, G, H | Metallo-beta-lactamase ndm-1 | protein | 228 | 24% helix, 32% strand | A0A0A7Y424 |
| D | Metallo-beta-lactamase ndm-1 | protein | 229 | 24% helix, 31% strand | A0A0A7Y424 |
Ligands and binding sites
- 8YL · (2S,3R)-2-[(2S,3R)-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-[(3S,5S)-5-(dimethylcarbamoyl) pyrrolidin-3-yl]sulfan yl-3-methyl-2,3-dihydro-1H-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
- SO4 · Sulfate ion · ion · 7 copies · chains A, E, B, C, D, H, G, F
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 | 1136 | 0.80 | 0.82 | 101 | 8YL, ZN |
| 2 | 106 | 0.79 | 0.99 | 22 | empty |
| 3 | 103 | 0.78 | 0.98 | 20 | empty |
| 4 | 533 | 0.67 | 0.78 | 72 | empty |
| 5 | 440 | 0.64 | 0.78 | 62 | empty |
Interfaces
15 interfaces between chains.
- B–G · 899 Ų buried · 4 hydrogen bonds · protein-protein
- D–F · 892 Ų buried · 4 hydrogen bonds · protein-protein
- A–H · 477 Ų buried · 2 hydrogen bonds · protein-protein
- C–E · 426 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 318 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5YPM · Crystal structure of NDM-1 bound to hydrolyzed meropenem 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 5YPM · PDBe 5YPM · UniProt A0A0A7Y424
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