MolNFT v1 · #107012 · protein
Complex of the X-domain and oxyb from teicoplanin biosynthesis
4TX3 · Oxyb protein: “Complex of the X-domain and oxyb from teicoplanin biosynthesis”. X-ray diffraction, 2 ligands (HEM, SO4), 9 pockets (best druggability 0.79). MolNFT v1 #107012 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4TX3
- Type
- protein
- Length
- 830 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxyb protein; Peptide synthetase, module 7
- EC
- 1.14.14.1
- UniProt
- Q70AY8, Q6ZZJ3
- Ligands
- HEM, SO4
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxyb protein (EC 1.14.14.1) | protein | 373 | 51% helix, 12% strand | Q70AY8 |
| B | Peptide synthetase, module 7 | protein | 457 | 35% helix, 21% strand | Q6ZZJ3 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1137 | 0.79 | 0.81 | 100 | empty |
| 2 | 731 | 0.78 | 0.82 | 73 | HEM, EDO |
| 3 | 720 | 0.77 | 0.82 | 56 | empty |
| 4 | 62 | 0.66 | 0.94 | 22 | empty |
| 5 | 110 | 0.65 | 0.89 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 785 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4TX3 · Complex of the X-domain and OxyB from Teicoplanin Biosynthesis · 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 Q70AY8
- Every structure of UniProt Q6ZZJ3
- Elsewhere: RCSB PDB 4TX3 · PDBe 4TX3 · UniProt Q70AY8 · UniProt Q6ZZJ3
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