MolNFT v1 · #106672 · protein
Cards toxin, nicked
4TLV · ADP-ribosylating toxin cards: “Cards toxin, nicked”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.85). MolNFT v1 #106672 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4TLV
- Type
- protein
- Length
- 3,471 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosylating toxin cards
- EC
- 2.4.2.-
- UniProt
- P75409
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 15% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | ADP-ribosylating toxin cards (EC 2.4.2.-) | protein | 582 | 15% helix, 36% strand | P75409 |
| B | ADP-ribosylating toxin cards (EC 2.4.2.-) | protein | 580 | 15% helix, 36% strand | P75409 |
| C | ADP-ribosylating toxin cards (EC 2.4.2.-) | protein | 577 | 15% helix, 37% strand | P75409 |
| D | ADP-ribosylating toxin cards (EC 2.4.2.-) | protein | 577 | 15% helix, 37% strand | P75409 |
| F | ADP-ribosylating toxin cards (EC 2.4.2.-) | protein | 573 | 15% helix, 37% strand | P75409 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, E, C, D
- GOL · Glycerol · additive · 27 copies · chains A, B, C, D, E, F
- ACT · Acetate ion · additive · 4 copies · chains A, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 628 | 0.85 | 0.89 | 68 | GOL |
| 2 | 599 | 0.84 | 0.89 | 87 | GOL |
| 3 | 522 | 0.83 | 0.89 | 72 | GOL |
| 4 | 1042 | 0.82 | 0.83 | 108 | SO4 |
| 5 | 275 | 0.77 | 0.90 | 54 | empty |
Interfaces
6 interfaces between chains.
- E–F · 1670 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1622 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1601 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 727 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 705 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
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 P75409
- Elsewhere: RCSB PDB 4TLV · PDBe 4TLV · UniProt P75409
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