MolNFT v1 · #87630 · protein
Ancestral pnca (last common ancestors of gram-positive and gram- negative bacteria) beta-lactamase class a
4C6Y: “Ancestral pnca (last common ancestors of gram-positive and gram- negative bacteria) beta-lactamase class a”. X-ray diffraction, 2 ligands (NA, CL), 4 pockets (best druggability 0.53). MolNFT v1 #87630 on GenesisL1: 3D structure…
- PDB
- 4C6Y
- 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
- Ligands
- NA, CL
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 262 | 45% helix, 18% strand | — |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 261 | 44% helix, 18% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 21 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
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 | 257 | 0.53 | 0.76 | 34 | PEG |
| 2 | 58 | 0.39 | 0.80 | 18 | CL |
| 3 | 60 | 0.31 | 0.76 | 14 | PEG |
| 4 | 52 | 0.28 | 0.75 | 11 | PEG, NA |
Interfaces
1 interface between chains.
- A–B · 885 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 4C6Y · Ancestral PNCA (last common ancestors of Gram-positive and Gram- negative bacteria)… · 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
- Elsewhere: RCSB PDB 4C6Y · PDBe 4C6Y
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