Research workbench
Crystal structure of SPBC2 prophage-derived protein yoms
Analyse Crystal structure of SPBC2 prophage-derived protein yoms in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6I5O
- Type
- protein
- Length
- 560 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SPBC2 prophage-derived uncharacterized protein yoms
- UniProt
- O31965
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 62% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | SPBC2 prophage-derived uncharacterized protein yoms | protein | 112 | 0% helix, 62% strand | O31965 |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 942 | 0.73 | 0.77 | 110 | empty |
| 2 | 120 | 0.50 | 0.80 | 26 | empty |
| 3 | 115 | 0.50 | 0.81 | 24 | empty |
| 4 | 99 | 0.46 | 0.80 | 17 | empty |
| 5 | 61 | 0.42 | 0.82 | 18 | empty |
Interfaces
10 interfaces between chains.
- B–C · 1170 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1170 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1156 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1152 Ų buried · 22 hydrogen bonds · protein-protein
- A–E · 1143 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 6I5O · Crystal structure of SPBc2 prophage-derived protein YomS · the same entry in another collection · chain A against A, TM-score 1.00
- O31965 · AlphaFold monomer V2.0 prediction for spbeta prophage-derived uncharacterized protein… · a predicted model of the same protein · chain A against A, TM-score 0.93
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 O31965
- Elsewhere: RCSB PDB 6I5O · PDBe 6I5O · UniProt O31965
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