MolNFT v1 · #77627 · protein
Crystal structure of new delhi metallo-beta-lactamase-1 from klebsiella pneumoniae
3RKK · Beta-lactamase ndm-1: “Crystal structure of new delhi metallo-beta-lactamase-1 from klebsiella pneumoniae”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.76). MolNFT v1 #77627 on GenesisL1: 3D structure, binding…
- PDB
- 3RKK
- Type
- protein
- Length
- 453 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase ndm-1
- EC
- 3.5.2.6
- UniProt
- C7C422
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase ndm-1 (EC 3.5.2.6) | protein | 227 | 26% helix, 25% strand | C7C422 |
| B | Beta-lactamase ndm-1 (EC 3.5.2.6) | protein | 226 | 25% helix, 30% strand | C7C422 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, B
- ACY · Acetic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 109 | 0.76 | 0.96 | 19 | empty |
| 2 | 187 | 0.51 | 0.78 | 31 | SO4, ACY |
| 3 | 119 | 0.43 | 0.76 | 29 | SO4 |
| 4 | 52 | 0.32 | 0.77 | 15 | empty |
| 5 | 54 | 0.32 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 980 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3RKK · Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 from Klebsiella pneumoniae · 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 0.98
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 3RKK · PDBe 3RKK · UniProt C7C422
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