Research workbench
Human transcription cofactor PC4 DNA-binding domain in complex with full phosphorothioate 5-10-5 2'-O-methyl DNA gapmer antisense oligonucleotide.
Analyse Human transcription cofactor PC4 DNA-binding domain in complex with full… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YCS
- Type
- protein + DNA
- Length
- 294 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PC4 protein; DNA (5'-D(P*(OKQ))-D(P*(OKT))-R(P*(RFJ))-D(*(OKQ)P*(OKT)…
- UniProt
- Q6IBA2
- Ligands
- NA, SO4
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 26% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PC4 protein | protein | 66 | 27% helix, 48% strand | Q6IBA2 |
| B | PC4 protein | protein | 67 | 25% helix, 48% strand | Q6IBA2 |
| C | PC4 protein | protein | 68 | 26% helix, 47% strand | Q6IBA2 |
| D | PC4 protein | protein | 65 | 26% helix, 46% strand | Q6IBA2 |
| E | DNA (5'-D(P*(OKQ))-D(P*(OKT))-R(P*(RFJ))-D(*(OKQ)P*(OKT) P*(AS)P*(GS)P*(OKN)P*(OKN)P*(PST)P*(OKN)P*(PST)P*(GS)P*(GS)P*(AS) P*(OKT)P*(OKT))-3') | dna | 16 | — | — |
| F | DNA (5'-D(P*(OKQ))-D(P*(OKT))-R(P*(RFJ))-D(*(OKQ)P*(OKT) P*(AS)P*(GS)P*(OKN)P*(OKN)P*(PST)P*(OKN)P*(PST)P*(GS)P*(GS)P*(AS) P*(OKT)P*(OKT))-3') | dna | 12 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 812 | 0.77 | 0.81 | 59 | SO4 |
| 2 | 203 | 0.50 | 0.76 | 20 | empty |
| 3 | 129 | 0.49 | 0.80 | 18 | empty |
| 4 | 68 | 0.38 | 0.79 | 17 | NA |
Interfaces
12 interfaces between chains.
- C–D · 1461 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1428 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 781 Ų buried · 14 hydrogen bonds · protein-nucleic
- D–F · 647 Ų buried · 13 hydrogen bonds · protein-nucleic
- E–F · 574 Ų buried · 32 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 28 modified (nucleotide modification).
Compared structures
- 6YCS · Human Transcription Cofactor PC4 DNA-binding domain in complex with full phosphorothioate… · 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 Q6IBA2
- Elsewhere: RCSB PDB 6YCS · PDBe 6YCS · UniProt Q6IBA2
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