MolNFT v1 · #112052 · protein
ECPLTA
4Z9D · Pertussis toxin-like subunit arta: “ECPLTA”. X-ray diffraction, 2 ligands (NAD, NA), 7 pockets (best druggability 0.77). MolNFT v1 #112052 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4Z9D
- Type
- protein
- Length
- 698 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pertussis toxin-like subunit arta
- EC
- 2.2.2.30
- UniProt
- A0A0B1KWV6
- Ligands
- NAD, NA
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pertussis toxin-like subunit arta (EC 2.2.2.30) | protein | 174 | 25% helix, 29% strand | A0A0B1KWV6 |
| B | Pertussis toxin-like subunit arta (EC 2.2.2.30) | protein | 174 | 25% helix, 29% strand | A0A0B1KWV6 |
| C, D | Pertussis toxin-like subunit arta (EC 2.2.2.30) | protein | 175 | 25% helix, 29% strand | A0A0B1KWV6 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 2 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1015 | 0.77 | 0.79 | 82 | NAD |
| 2 | 468 | 0.67 | 0.79 | 42 | NAD |
| 3 | 430 | 0.67 | 0.79 | 45 | NAD |
| 4 | 287 | 0.65 | 0.81 | 42 | empty |
| 5 | 461 | 0.64 | 0.77 | 43 | NAD |
Interfaces
4 interfaces between chains.
- B–C · 938 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 896 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 641 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 335 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4Z9D · EcPltA · 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
- Elsewhere: RCSB PDB 4Z9D · PDBe 4Z9D · UniProt A0A0B1KWV6
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