MolNFT v1 · #1309 · protein
Mature oxy-cope catalytic antibody with hapten
1AXS: “Mature oxy-cope catalytic antibody with hapten”. X-ray diffraction, 2 ligands (HOP, CD), 10 pockets (best druggability 0.68). MolNFT v1 #1309 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1AXS
- Type
- protein
- Length
- 864 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxy-cope catalytic antibody
- UniProt
- P01857
- Ligands
- HOP, CD
- Pockets
- 10 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A | Oxy-cope catalytic antibody | protein | 211 | 4% helix, 50% strand | — |
| H, B | Oxy-cope catalytic antibody | protein | 221 | 5% helix, 48% strand | P01857 |
Ligands and binding sites
- HOP · (1S,2S,5S)2-(4-glutaridylbenzyl)-5-phenyl-1-cyclohexanol · ligand · 2 copies · chains L, H, A, B
- CD · Cadmium ion · metal · 8 copies · chains L, H, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 94 | 0.68 | 0.91 | 18 | HOP |
| 2 | 113 | 0.63 | 0.87 | 21 | HOP |
| 3 | 511 | 0.58 | 0.73 | 48 | empty |
| 4 | 320 | 0.51 | 0.73 | 37 | empty |
| 5 | 182 | 0.45 | 0.74 | 20 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1771 Ų buried · 16 hydrogen bonds · protein-protein
- L–H · 1722 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1AXS · Mature oxy-cope catalytic antibody with hapten · the same entry in another collection · chain H against H, 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 P01857
- Elsewhere: RCSB PDB 1AXS · PDBe 1AXS · UniProt P01857
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