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Crystal structure of ndm-12 metallo-beta-lactamase in complex with hydrolyzed ampicillin
Analyse Crystal structure of ndm-12 metallo-beta-lactamase in complex with hydrolyzed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OL8
- Type
- protein
- Length
- 480 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallo-beta-lactamase ndm-12
- UniProt
- A0A024FRL9
- Ligands
- ZZ7, ZN, NA, CL
- Pockets
- 4 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Metallo-beta-lactamase ndm-12 | protein | 240 | 25% helix, 31% strand | A0A024FRL9 |
Ligands and binding sites
- ZZ7 · (2R,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 5 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 | 229 | 0.52 | 0.76 | 28 | CL |
| 2 | 122 | 0.47 | 0.79 | 17 | empty |
| 3 | 177 | 0.45 | 0.74 | 27 | ZZ7 |
| 4 | 138 | 0.41 | 0.74 | 22 | ZN, ZZ7 |
Interfaces
1 interface between chains.
- A–B · 326 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6OL8 · Crystal structure of NDM-12 metallo-beta-lactamase in complex with hydrolyzed ampicillin · 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 A0A024FRL9
- Elsewhere: RCSB PDB 6OL8 · PDBe 6OL8 · UniProt A0A024FRL9
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