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Crystal structure of rst D1-D2
Analyse Crystal structure of rst D1-D2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OF8
- Type
- protein
- Length
- 839 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Irregular chiasm C-roughest protein
- UniProt
- Q08180
- Ligands
- NA
- Pockets
- 9 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Irregular chiasm C-roughest protein | protein | 211 | 3% helix, 50% strand | Q08180 |
| B, D | Irregular chiasm C-roughest protein | protein | 209 | 3% helix, 49% strand | Q08180 |
| C | Irregular chiasm C-roughest protein | protein | 210 | 3% helix, 49% strand | Q08180 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 6 copies · chains A, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 518 | 0.66 | 0.78 | 60 | NA, GOL |
| 2 | 432 | 0.66 | 0.79 | 48 | empty |
| 3 | 55 | 0.39 | 0.81 | 19 | empty |
| 4 | 122 | 0.35 | 0.72 | 28 | empty |
| 5 | 93 | 0.35 | 0.74 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 682 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 655 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 654 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 58 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 56 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
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 Q08180
- Elsewhere: RCSB PDB 4OF8 · PDBe 4OF8 · UniProt Q08180
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