MolNFT v1 · #103137 · protein
Antitoxin HICB3 crystal structure
4P7D: “Antitoxin HICB3 crystal structure”. X-ray diffraction, 1 ligand (CL), 7 pockets (best druggability 0.64). MolNFT v1 #103137 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4P7D
- Type
- protein
- Length
- 543 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antitoxin HICB3
- UniProt
- Q0WBS6
- Ligands
- CL
- Pockets
- 7 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Antitoxin HICB3 | protein | 135 | 43% helix, 24% strand | Q0WBS6 |
| B | Antitoxin HICB3 | protein | 137 | 41% helix, 22% strand | Q0WBS6 |
| D | Antitoxin HICB3 | protein | 136 | 40% helix, 23% strand | Q0WBS6 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains B, C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 538 | 0.64 | 0.76 | 47 | empty |
| 2 | 487 | 0.63 | 0.76 | 46 | empty |
| 3 | 170 | 0.56 | 0.80 | 24 | CL |
| 4 | 126 | 0.53 | 0.81 | 23 | CL |
| 5 | 109 | 0.38 | 0.75 | 24 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2160 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 2078 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1157 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 1070 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 165 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 4P7D · Antitoxin HicB3 crystal structure · 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 Q0WBS6
- Elsewhere: RCSB PDB 4P7D · PDBe 4P7D · UniProt Q0WBS6
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