MolNFT v1 · #79048 · protein
New delhi metallo-beta-lactamase-1 complexed with CD
3SRX · Beta-lactamase ndm-1: “New delhi metallo-beta-lactamase-1 complexed with CD”. X-ray diffraction, 3 ligands (CD, CL, SCN), 4 pockets (best druggability 0.67). MolNFT v1 #79048 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3SRX
- Type
- protein
- Length
- 466 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
- CD, CL, SCN
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase ndm-1 (EC 3.5.2.6) | protein | 237 | 24% helix, 30% strand | C7C422 |
| B | Beta-lactamase ndm-1 (EC 3.5.2.6) | protein | 229 | 27% helix, 32% strand | C7C422 |
Ligands and binding sites
- CD · Cadmium ion · metal · 6 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- SCN · Thiocyanate ion · ion · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 425 | 0.67 | 0.79 | 49 | GOL, SCN |
| 2 | 110 | 0.39 | 0.75 | 24 | CD, CL |
| 3 | 109 | 0.39 | 0.75 | 19 | empty |
| 4 | 113 | 0.39 | 0.75 | 22 | CD, CL |
Interfaces
1 interface between chains.
- A–B · 458 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
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 3SRX · PDBe 3SRX · UniProt C7C422
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