MolNFT v1 · #112051 · protein
Ecpltab oxidized
4Z9C · Pertussis toxin-like subunit arta: “Ecpltab oxidized”. X-ray diffraction, 1 ligand (PO4), 9 pockets (best druggability 0.76). MolNFT v1 #112051 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4Z9C
- Type
- protein
- Length
- 798 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pertussis toxin-like subunit arta; Subtilase cytotoxin subunit B-like protein
- EC
- 2.4.2.30
- UniProt
- A0A0B1KWV6, A0A0B1KTJ4
- Ligands
- PO4
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pertussis toxin-like subunit arta (EC 2.4.2.30) | protein | 223 | 29% helix, 26% strand | A0A0B1KWV6 |
| B, C, D, E, F | Subtilase cytotoxin subunit B-like protein | protein | 115 | 17% helix, 50% strand | A0A0B1KTJ4 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1107 | 0.76 | 0.78 | 87 | empty |
| 2 | 321 | 0.73 | 0.86 | 38 | empty |
| 3 | 745 | 0.69 | 0.76 | 65 | empty |
| 4 | 51 | 0.45 | 0.83 | 10 | empty |
| 5 | 146 | 0.44 | 0.76 | 23 | empty |
Interfaces
10 interfaces between chains.
- D–E · 1056 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1037 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1011 Ų buried · 15 hydrogen bonds · protein-protein
- B–F · 967 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 934 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide (disulfide).
Compared structures
- 4Z9C · EcPltAB Oxidized · 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 A0A0B1KWV6
- Every structure of UniProt A0A0B1KTJ4
- Elsewhere: RCSB PDB 4Z9C · PDBe 4Z9C · UniProt A0A0B1KWV6 · UniProt A0A0B1KTJ4
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