MolNFT v1 · #54117 · protein
Structural and mechanistic studies on a cephalosporin esterase from the clavulanic acid biosynthesis pathway
2XF3 · ORF12: “Structural and mechanistic studies on a cephalosporin esterase from the clavulanic acid biosynthesis pathway”. X-ray diffraction, 1 ligand (J01), 14 pockets (best druggability 0.74). MolNFT v1 #54117 on GenesisL1: 3D…
- PDB
- 2XF3
- Type
- protein
- Length
- 851 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ORF12
- UniProt
- Q83Z62
- Ligands
- J01
- Pockets
- 14 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ORF12 | protein | 423 | 45% helix, 22% strand | Q83Z62 |
| B | ORF12 | protein | 428 | 45% helix, 21% strand | Q83Z62 |
Ligands and binding sites
- J01 · (2R,3Z,5R)-3-(2-hydroxyethylidene)-7-oxo-4-oxa-1-azabicyclo[3.2.0]heptane-2-carboxylic acid · ligand · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 646 | 0.74 | 0.80 | 61 | J01 |
| 2 | 578 | 0.72 | 0.80 | 60 | J01 |
| 3 | 61 | 0.71 | 0.98 | 24 | empty |
| 4 | 319 | 0.61 | 0.78 | 29 | J01 |
| 5 | 303 | 0.61 | 0.78 | 29 | J01 |
Interfaces
1 interface between chains.
- A–B · 749 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2XF3 · Structural and mechanistic studies on a cephalosporin esterase from the clavulanic acid… · 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 Q83Z62
- Elsewhere: RCSB PDB 2XF3 · PDBe 2XF3 · UniProt Q83Z62
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