MolNFT v1 · #166989 · protein
Structure of ctx-M-14 bound to vaborbactam at 1.0 a
6V7H · Beta-lactamase: “Structure of ctx-M-14 bound to vaborbactam at 1.0 a”. X-ray diffraction, 4 ligands (4D6, WXM, K), 2 pockets (best druggability 0.78). MolNFT v1 #166989 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6V7H
- Type
- protein
- Length
- 523 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- A0A2S1PK93
- Ligands
- 4D6, WXM, K, PO4
- Pockets
- 2 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 263 | 44% helix, 19% strand | A0A2S1PK93 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 260 | 43% helix, 20% strand | A0A2S1PK93 |
Ligands and binding sites
- 4D6 · Vaborbactam · ligand · 2 copies · chains A, B
- WXM · 2-[(3~{R},6~{S})-2,2-bis(oxidanyl)-3-(2-thiophen-2-ylethanoylamino)-1-oxa-2-boranuidacyclohex-6-yl]ethanoic acid · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 962 | 0.78 | 0.80 | 102 | 4D6 |
| 2 | 122 | 0.36 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 636 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 modified (covalent ligand, cyclization).
Compared structures
- 6V7H · Structure of CTX-M-14 bound to Vaborbactam at 1.0 A · 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 A0A2S1PK93
- Elsewhere: RCSB PDB 6V7H · PDBe 6V7H · UniProt A0A2S1PK93
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