MolNFT v1 · #58887 · protein
Crystal structure of protein DIP2346 from corynebacterium diphtheriae
3BH1 · UPF0371 protein DIP2346: “Crystal structure of protein DIP2346 from corynebacterium diphtheriae”. X-ray diffraction, 20 pockets (best druggability 0.77). MolNFT v1 #58887 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3BH1
- Type
- protein
- Length
- 1,942 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UPF0371 protein DIP2346
- UniProt
- Q6NEC9
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | UPF0371 protein DIP2346 | protein | 486 | 49% helix, 14% strand | Q6NEC9 |
| C | UPF0371 protein DIP2346 | protein | 483 | 48% helix, 14% strand | Q6NEC9 |
| D | UPF0371 protein DIP2346 | protein | 487 | 48% helix, 14% strand | Q6NEC9 |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 971 | 0.77 | 0.79 | 94 | GOL |
| 2 | 558 | 0.73 | 0.81 | 66 | empty |
| 3 | 72 | 0.73 | 0.97 | 23 | empty |
| 4 | 214 | 0.73 | 0.89 | 35 | empty |
| 5 | 874 | 0.73 | 0.77 | 71 | GOL |
Interfaces
6 interfaces between chains.
- A–B · 1154 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 950 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 884 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 819 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 260 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3BH1 · Crystal structure of protein DIP2346 from Corynebacterium diphtheriae · the same entry in another collection · chain A against A, TM-score 1.00
- Q6NEC9 · AlphaFold monomer V2.0 prediction for UPF0371 protein DIP2346 (Q6NEC9) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q6NEC9
- Elsewhere: RCSB PDB 3BH1 · PDBe 3BH1 · UniProt Q6NEC9
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