Research workbench
Crystal structure of SEL1 repeat protein from oxalobacter formigenes
Analyse Crystal structure of SEL1 repeat protein from oxalobacter formigenes in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OK3
- Type
- protein
- Length
- 1,015 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SEL1 repeat protein
- EC
- 3.5.2.6
- UniProt
- C3X9N1
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.32
Structure
x-ray diffraction · 2 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SEL1 repeat protein (EC 3.5.2.6) | protein | 509 | 72% helix, 0% strand | C3X9N1 |
| B | SEL1 repeat protein (EC 3.5.2.6) | protein | 506 | 71% helix, 0% strand | C3X9N1 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B
- PGE · Triethylene glycol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.32 | 0.73 | 20 | empty |
| 2 | 78 | 0.31 | 0.73 | 12 | empty |
| 3 | 54 | 0.30 | 0.76 | 15 | empty |
| 4 | 58 | 0.28 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 340 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified, 4 disulfide (methylation, engineered, disulfide).
Compared structures
- 6OK3 · Crystal structure of Sel1 repeat protein from Oxalobacter formigenes · 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 C3X9N1
- Elsewhere: RCSB PDB 6OK3 · PDBe 6OK3 · UniProt C3X9N1
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