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Crystal structure of NDM-1 metallo-beta-lactamase harboring an insertion of a Pro residue in L3 loop
Analyse Crystal structure of NDM-1 metallo-beta-lactamase harboring an insertion of a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CAC
- Type
- protein
- Length
- 928 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.79
- Source
- Klebsiella pneumoniae
- Molecule
- Metallo-beta-lactamase type 2
- EC
- 3.5.2.6
- UniProt
- C7C422
- Ligands
- NI, ZN, CD, CO, CA, SO4
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · resolution 1.79 · 3 distinct chains · 24% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Metallo-beta-lactamase type 2 (EC 3.5.2.6) | protein | 234 | 25% helix, 31% strand | C7C422 |
| B | Metallo-beta-lactamase type 2 (EC 3.5.2.6) | protein | 229 | 24% helix, 32% strand | C7C422 |
| D | Metallo-beta-lactamase type 2 (EC 3.5.2.6) | protein | 231 | 23% helix, 30% strand | C7C422 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 5 copies · chains A, D, B, C
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- CD · Cadmium ion · metal · 4 copies · chains A, B, C, D
- CO · Cobalt (II) ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 109 | 0.77 | 0.97 | 20 | empty |
| 2 | 107 | 0.77 | 0.97 | 22 | empty |
| 3 | 527 | 0.60 | 0.74 | 56 | SO4 |
| 4 | 106 | 0.55 | 0.84 | 32 | empty |
| 5 | 97 | 0.54 | 0.85 | 32 | empty |
Interfaces
4 interfaces between chains.
- C–D · 890 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 883 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 240 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 111 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6CAC · Crystal structure of ndm-1 metallo-beta-lactamase harboring an insertion of a pro residue… · 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 D against A, TM-score 0.97
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 6CAC · PDBe 6CAC · UniProt C7C422
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