Research workbench
Crystal structure of hypothetical protein OPAG_01669 from rhodococcus opacus PD630, target 016205
Analyse Crystal structure of hypothetical protein OPAG_01669 from rhodococcus opacus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IX1
- Type
- protein
- Length
- 1,865 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein
- Ligands
- PO4
- Pockets
- 20 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hypothetical protein | protein | 234 | 48% helix, 16% strand | — |
| C, D, G | Hypothetical protein | protein | 233 | 48% helix, 16% strand | — |
| E, H | Hypothetical protein | protein | 233 | 47% helix, 17% strand | — |
| F | Hypothetical protein | protein | 232 | 49% helix, 16% strand | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, E, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 446 | 0.67 | 0.79 | 43 | empty |
| 2 | 543 | 0.66 | 0.76 | 71 | empty |
| 3 | 315 | 0.63 | 0.79 | 37 | empty |
| 4 | 402 | 0.63 | 0.77 | 36 | empty |
| 5 | 328 | 0.61 | 0.78 | 37 | empty |
Interfaces
12 interfaces between chains.
- B–F · 1013 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 972 Ų buried · 11 hydrogen bonds · protein-protein
- D–H · 971 Ų buried · 10 hydrogen bonds · protein-protein
- C–G · 964 Ų buried · 10 hydrogen bonds · protein-protein
- A–H · 474 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 4IX1 · Crystal structure of hypothetical protein OPAG_01669 from Rhodococcus Opacus PD630… · 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
- Elsewhere: RCSB PDB 4IX1 · PDBe 4IX1
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