MolNFT v1 · #144906 · protein
Ndm-1 beta-lactamase exhibits differential active site sequence requirements for the hydrolysis of penicillin versus carbapenem antibiotics
6C89: “Ndm-1 beta-lactamase exhibits differential active site sequence requirements for the hydrolysis of penicillin…”. X-ray diffraction, 3 ligands (ZN, NA, CL), 7 pockets (best druggability 0.80). MolNFT v1 #144906 on GenesisL1: 3D…
- PDB
- 6C89
- Type
- protein
- Length
- 917 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- UniProt
- E5KIY2
- Ligands
- ZN, NA, CL
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Beta-lactamase | protein | 231 | 26% helix, 30% strand | E5KIY2 |
| B | Beta-lactamase | protein | 227 | 24% helix, 30% strand | E5KIY2 |
| C | Beta-lactamase | protein | 228 | 24% helix, 33% strand | E5KIY2 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- NA · Sodium ion · metal · 2 copies · chains A, B, C
- CL · Chloride ion · ion · 2 copies · chains B, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, D
- GOL · Glycerol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.80 | 0.99 | 22 | empty |
| 2 | 111 | 0.78 | 0.98 | 20 | empty |
| 3 | 1060 | 0.74 | 0.77 | 98 | NA, CL, GOL |
| 4 | 572 | 0.66 | 0.77 | 57 | CL |
| 5 | 109 | 0.43 | 0.77 | 19 | ZN |
Interfaces
5 interfaces between chains.
- C–D · 1036 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1031 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 318 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 184 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 156 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6C89 · NDM-1 Beta-Lactamase Exhibits Differential Active Site Sequence Requirements for the… · 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 E5KIY2
- Elsewhere: RCSB PDB 6C89 · PDBe 6C89 · UniProt E5KIY2
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