Research workbench
Crystal structure of ndm-9 metallo-beta-lactamase
Analyse Crystal structure of ndm-9 metallo-beta-lactamase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OGO
- Type
- protein
- Length
- 685 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Subclass B1 metallo-beta-lactamase ndm-9
- UniProt
- A0A1M2CSI6
- Ligands
- ZN, CL, PO4
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Subclass B1 metallo-beta-lactamase ndm-9 | protein | 229 | 25% helix, 32% strand | A0A1M2CSI6 |
| B | Subclass B1 metallo-beta-lactamase ndm-9 | protein | 229 | 24% helix, 32% strand | A0A1M2CSI6 |
| C | Subclass B1 metallo-beta-lactamase ndm-9 | protein | 227 | 26% helix, 32% strand | A0A1M2CSI6 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C
- CL · Chloride ion · ion · 9 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B, C
- PGE · Triethylene glycol · additive · 2 copies · chains A, C
- GOL · Glycerol · additive · 2 copies · chains B, C
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 | 416 | 0.62 | 0.77 | 52 | GOL, CL |
| 2 | 296 | 0.53 | 0.75 | 25 | empty |
| 3 | 91 | 0.35 | 0.75 | 22 | ZN, CL, PO4 |
| 4 | 69 | 0.33 | 0.76 | 15 | CL, EDO |
| 5 | 54 | 0.29 | 0.76 | 15 | CL, PGE |
Interfaces
2 interfaces between chains.
- B–C · 278 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 192 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6OGO · Crystal structure of NDM-9 metallo-beta-lactamase · 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 A0A1M2CSI6
- Elsewhere: RCSB PDB 6OGO · PDBe 6OGO · UniProt A0A1M2CSI6
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