Research workbench
Structure of a cdps from fluoribacter dumoffii
Analyse Structure of a cdps from fluoribacter dumoffii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OCD
- Type
- protein
- Length
- 2,242 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclodipeptide synthase
- UniProt
- A0A0W0T5C6
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 8 distinct chains · 57% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cyclodipeptide synthase | protein | 226 | 58% helix, 17% strand | A0A0W0T5C6 |
| C | Cyclodipeptide synthase | protein | 226 | 57% helix, 17% strand | A0A0W0T5C6 |
| D | Cyclodipeptide synthase | protein | 225 | 58% helix, 16% strand | A0A0W0T5C6 |
| E | Cyclodipeptide synthase | protein | 224 | 55% helix, 17% strand | A0A0W0T5C6 |
| F | Cyclodipeptide synthase | protein | 220 | 55% helix, 16% strand | A0A0W0T5C6 |
| G | Cyclodipeptide synthase | protein | 221 | 57% helix, 17% strand | A0A0W0T5C6 |
| H | Cyclodipeptide synthase | protein | 226 | 56% helix, 16% strand | A0A0W0T5C6 |
| I, J | Cyclodipeptide synthase | protein | 224 | 57% helix, 17% strand | A0A0W0T5C6 |
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 | 851 | 0.73 | 0.78 | 75 | empty |
| 2 | 660 | 0.73 | 0.79 | 65 | empty |
| 3 | 509 | 0.69 | 0.79 | 58 | empty |
| 4 | 578 | 0.68 | 0.78 | 62 | empty |
| 5 | 565 | 0.67 | 0.77 | 59 | empty |
Interfaces
11 interfaces between chains.
- A–E · 524 Ų buried · 5 hydrogen bonds · protein-protein
- D–J · 502 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 500 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 492 Ų buried · 7 hydrogen bonds · protein-protein
- E–H · 463 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5OCD · structure of a CDPS from Fluoribacter dumoffii · 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 A0A0W0T5C6
- Elsewhere: RCSB PDB 5OCD · PDBe 5OCD · UniProt A0A0W0T5C6
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