Research workbench
Ocpa complexed cprk (C200S)
Analyse Ocpa complexed cprk (C200S) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3E5U
- Type
- protein
- Length
- 872 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclic nucleotide-binding protein
- UniProt
- Q18R04
- Ligands
- 3C4, NA, PO4
- Pockets
- 18 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Cyclic nucleotide-binding protein | protein | 219 | 40% helix, 25% strand | Q18R04 |
| A | Cyclic nucleotide-binding protein | protein | 215 | 40% helix, 25% strand | Q18R04 |
| D | Cyclic nucleotide-binding protein | protein | 220 | 40% helix, 28% strand | Q18R04 |
| B | Cyclic nucleotide-binding protein | protein | 218 | 40% helix, 25% strand | Q18R04 |
Ligands and binding sites
- 3C4 · (3-chloro-4-hydroxyphenyl)acetic acid · ligand · 5 copies · chains C, D, A, B
- NA · Sodium ion · metal · chains A, B
- PO4 · Phosphate ion · ion · 3 copies · chains C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.76 | 0.98 | 16 | 3C4 |
| 2 | 65 | 0.74 | 0.98 | 16 | 3C4 |
| 3 | 65 | 0.73 | 0.98 | 18 | 3C4 |
| 4 | 66 | 0.73 | 0.97 | 16 | 3C4 |
| 5 | 904 | 0.69 | 0.75 | 84 | NA |
Interfaces
5 interfaces between chains.
- C–D · 2414 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 2373 Ų buried · 25 hydrogen bonds · protein-protein
- C–B · 392 Ų buried · 9 hydrogen bonds · protein-protein
- C–A · 130 Ų buried · 0 hydrogen bonds · protein-protein
- D–B · 113 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3E5U · OCPA complexed CprK (C200S) · the same entry in another collection · chain C against C, 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 Q18R04
- Elsewhere: RCSB PDB 3E5U · PDBe 3E5U · UniProt Q18R04
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