Research workbench
Crystal structure of the new deli metallo beta lactamase variant 3 from klebsiella pneumoniae
Analyse Crystal structure of the new deli metallo beta lactamase variant 3 from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MH0
- Type
- protein
- Length
- 464 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallo-beta-lactamase ndm-3
- UniProt
- I3VKD5
- Ligands
- ZN, CL, SO4
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metallo-beta-lactamase ndm-3 | protein | 229 | 26% helix, 31% strand | I3VKD5 |
| B | Metallo-beta-lactamase ndm-3 | protein | 235 | 28% helix, 30% strand | I3VKD5 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · 8 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.77 | 0.97 | 20 | empty |
| 2 | 70 | 0.47 | 0.83 | 18 | empty |
| 3 | 91 | 0.43 | 0.79 | 17 | empty |
| 4 | 71 | 0.33 | 0.75 | 22 | SO4, CL |
| 5 | 53 | 0.29 | 0.75 | 20 | ZN, SO4, CL |
Interfaces
1 interface between chains.
- A–B · 871 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6MH0 · Crystal Structure of the New Deli Metallo Beta Lactamase Variant 3 from Klebsiella… · 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 I3VKD5
- Elsewhere: RCSB PDB 6MH0 · PDBe 6MH0 · UniProt I3VKD5
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