Research workbench
Crystal structure of the CTF18-1-8 module from CTF18-rfc
Analyse Crystal structure of the CTF18-1-8 module from CTF18-rfc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OKC
- Type
- protein
- Length
- 1,059 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sister chromatid cohesion protein DCC1; Chromosome transmission fidelity protein 8…
- UniProt
- P25559, P38877, P49956
- Ligands
- NO3
- Pockets
- 14 · best druggability 0.56
Structure
x-ray diffraction · 6 distinct chains · 28% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sister chromatid cohesion protein DCC1 | protein | 369 | 36% helix, 24% strand | P25559 |
| B | Sister chromatid cohesion protein DCC1 | protein | 377 | 35% helix, 24% strand | P25559 |
| F | Chromosome transmission fidelity protein 8 | protein | 132 | 11% helix, 55% strand | P38877 |
| G | Chromosome transmission fidelity protein 18 | protein | 26 | 15% helix, 27% strand | P49956 |
| H | Chromosome transmission fidelity protein 8 | protein | 128 | 12% helix, 56% strand | P38877 |
| I | Chromosome transmission fidelity protein 18 | protein | 27 | 15% helix, 26% strand | P49956 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 390 | 0.56 | 0.74 | 26 | empty |
| 2 | 100 | 0.52 | 0.83 | 19 | empty |
| 3 | 82 | 0.51 | 0.84 | 21 | empty |
| 4 | 154 | 0.48 | 0.77 | 22 | NO3 |
| 5 | 141 | 0.46 | 0.77 | 23 | NO3 |
Interfaces
7 interfaces between chains.
- A–H · 2833 Ų buried · 47 hydrogen bonds · protein-protein
- B–F · 2828 Ų buried · 49 hydrogen bonds · protein-protein
- H–I · 1104 Ų buried · 17 hydrogen bonds · protein-protein
- F–G · 1035 Ų buried · 17 hydrogen bonds · protein-protein
- A–I · 973 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 34 modified (engineered).
Compared structures
- 5OKC · Crystal structure of the Ctf18-1-8 module from Ctf18-RFC · the same entry in another collection · chain I against I, TM-score 1.00
- P25559 · AlphaFold monomer V2.0 prediction for sister chromatid cohesion protein DCC1 (P25559) · a predicted model of the same protein · chain A against A, TM-score 0.92
- P38877 · AlphaFold monomer V2.0 prediction for chromosome transmission fidelity protein 8 (P38877) · a predicted model of the same protein · chain H against A, TM-score 0.85
- P49956 · AlphaFold monomer V2.0 prediction for chromosome transmission fidelity protein 18 (P49956) · a predicted model of the same protein · chain G against A, TM-score 0.35
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 P25559
- Every structure of UniProt P38877
- Every structure of UniProt P49956
- Elsewhere: RCSB PDB 5OKC · PDBe 5OKC · UniProt P25559 · UniProt P38877 · UniProt P49956
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