MolNFT v1 · #159273 · protein
Crystal structure of SEL1 repeat protein from oxalobacter formigenes
6OK0: “Crystal structure of SEL1 repeat protein from oxalobacter formigenes”. X-ray diffraction, 1 ligand (CL), 5 pockets (best druggability 0.63). MolNFT v1 #159273 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6OK0
- Type
- protein
- Length
- 525 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SEL1 repeat protein
- EC
- 3.5.2.6
- UniProt
- C3X8T2
- Ligands
- CL
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 65% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | SEL1 repeat protein (EC 3.5.2.6) | protein | 131 | 66% helix, 0% strand | C3X8T2 |
| D | SEL1 repeat protein (EC 3.5.2.6) | protein | 132 | 65% helix, 0% strand | C3X8T2 |
Ligands and binding sites
- CL · Chloride ion · ion · chains A, D
- PGE · Triethylene glycol · additive · chains C
- IMD · Imidazole · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 357 | 0.63 | 0.78 | 46 | empty |
| 2 | 378 | 0.61 | 0.77 | 58 | empty |
| 3 | 101 | 0.45 | 0.79 | 25 | empty |
| 4 | 90 | 0.40 | 0.77 | 22 | empty |
| 5 | 100 | 0.37 | 0.75 | 24 | empty |
Interfaces
4 interfaces between chains.
- B–C · 471 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 471 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 305 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 246 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 modified (engineered, methylation).
Compared structures
- 6OK0 · 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 C3X8T2
- Elsewhere: RCSB PDB 6OK0 · PDBe 6OK0 · UniProt C3X8T2
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