Research workbench
Crystal structure of HCR/D F1240A mutant
Analyse Crystal structure of HCR/D F1240A mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RMX
- Type
- protein
- Length
- 1,620 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Botulinum neurotoxin type D
- UniProt
- P19321
- Pockets
- 19 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Botulinum neurotoxin type D | protein | 404 | 7% helix, 42% strand | P19321 |
| B | Botulinum neurotoxin type D | protein | 407 | 7% helix, 41% strand | P19321 |
| C | Botulinum neurotoxin type D | protein | 403 | 6% helix, 40% strand | P19321 |
| D | Botulinum neurotoxin type D | protein | 406 | 7% helix, 43% strand | P19321 |
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 930 | 0.77 | 0.80 | 81 | empty |
| 2 | 53 | 0.75 | 0.99 | 13 | empty |
| 3 | 1112 | 0.74 | 0.77 | 91 | empty |
| 4 | 353 | 0.72 | 0.84 | 43 | empty |
| 5 | 245 | 0.70 | 0.86 | 35 | empty |
Interfaces
5 interfaces between chains.
- A–D · 885 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 795 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 662 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 596 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 70 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3RMX · Crystal structure of HCR/D F1240A mutant · 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 P19321
- Elsewhere: RCSB PDB 3RMX · PDBe 3RMX · UniProt P19321
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