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Crystal structure of the mono-zinc-boundform of new delhi metallo- beta-lactamase-1 from klebsiella pneumoniae
Analyse Crystal structure of the mono-zinc-boundform of new delhi metallo… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SFP
- Type
- protein
- Length
- 925 residues
- Chains
- 4
- 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
- ZN, SO4, CL
- Pockets
- 6 · best druggability 0.40
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Beta-lactamase ndm-1 (EC 3.5.2.6) | protein | 231 | 27% helix, 30% strand | C7C422 |
| D | Beta-lactamase ndm-1 (EC 3.5.2.6) | protein | 232 | 26% helix, 30% strand | C7C422 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C
- CL · Chloride ion · ion · chains C
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
- CIT · Citric acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.40 | 0.74 | 24 | empty |
| 2 | 128 | 0.40 | 0.74 | 23 | CL |
| 3 | 87 | 0.34 | 0.74 | 20 | ZN |
| 4 | 51 | 0.31 | 0.77 | 14 | GOL |
| 5 | 50 | 0.30 | 0.76 | 14 | empty |
Compared structures
- 3SFP · Crystal Structure of the Mono-Zinc-boundform of New Delhi Metallo-beta-Lactamase-1 from… · the same entry in another collection · chain D against D, 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 C against A, TM-score 0.99
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 3SFP · PDBe 3SFP · UniProt C7C422
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