Research workbench
Conserved hypothetical protein from pyrococcus furiosus pfu-403030-001
Analyse Conserved hypothetical protein from pyrococcus furiosus pfu-403030-001 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XX7
- Type
- protein
- Length
- 1,008 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxetanocin-like protein
- UniProt
- Q8U3R1
- Ligands
- NI, UNX
- Pockets
- 9 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 71% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Oxetanocin-like protein | protein | 172 | 73% helix, 1% strand | Q8U3R1 |
| D | Oxetanocin-like protein | protein | 161 | 71% helix, 1% strand | Q8U3R1 |
| E | Oxetanocin-like protein | protein | 166 | 70% helix, 1% strand | Q8U3R1 |
| F | Oxetanocin-like protein | protein | 165 | 72% helix, 1% strand | Q8U3R1 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- UNX · Unknown atom or ion · ion · 19 copies · chains A, C, B, D, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 908 | 0.88 | 0.90 | 129 | UNX |
| 2 | 239 | 0.64 | 0.83 | 31 | UNX |
| 3 | 240 | 0.64 | 0.82 | 33 | empty |
| 4 | 344 | 0.62 | 0.78 | 35 | empty |
| 5 | 263 | 0.61 | 0.80 | 31 | empty |
Interfaces
12 interfaces between chains.
- C–D · 1924 Ų buried · 15 hydrogen bonds · protein-protein
- A–F · 1919 Ų buried · 14 hydrogen bonds · protein-protein
- B–E · 1854 Ų buried · 13 hydrogen bonds · protein-protein
- B–F · 967 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 949 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1XX7 · Conserved hypothetical protein from Pyrococcus furiosus Pfu-403030-001 · the same entry in another collection · chain D against D, 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 Q8U3R1
- Elsewhere: RCSB PDB 1XX7 · PDBe 1XX7 · UniProt Q8U3R1
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