Research workbench
B.SUBTILIS ytbe
Analyse B.SUBTILIS ytbe in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B3D
- Type
- protein
- Length
- 837 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative morphine dehydrogenase
- UniProt
- O34678
- Ligands
- CA
- Pockets
- 8 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Putative morphine dehydrogenase | protein | 280 | 43% helix, 17% strand | O34678 |
| B | Putative morphine dehydrogenase | protein | 277 | 45% helix, 16% strand | O34678 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 442 | 0.61 | 0.76 | 60 | empty |
| 2 | 203 | 0.53 | 0.77 | 40 | CA |
| 3 | 227 | 0.50 | 0.75 | 29 | empty |
| 4 | 77 | 0.47 | 0.82 | 22 | empty |
| 5 | 110 | 0.43 | 0.77 | 27 | CA |
Interfaces
3 interfaces between chains.
- A–C · 678 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 317 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 11 Ų buried · 0 hydrogen bonds · protein-protein
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 O34678
- Elsewhere: RCSB PDB 3B3D · PDBe 3B3D · UniProt O34678
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