Research workbench
Crystal structure of a ternary complex containing an oca-B peptide, the oct-1 pou domain, and an octamer element
Analyse Crystal structure of a ternary complex containing an oca-B peptide, the oct-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1CQT
- Type
- protein + DNA
- Length
- 366 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*TP*GP*TP*AP*TP*GP*CP*AP*AP*AP*TP*AP*AP*GP*G)-3'); DNA (5'…
- UniProt
- P14859, Q16633
- Pockets
- 11 · best druggability 0.62
Structure
x-ray diffraction · 8 distinct chains · 59% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| M | DNA (5'- D(*TP*GP*TP*AP*TP*GP*CP*AP*AP*AP*TP*AP*AP*GP*G)-3') | dna | 15 | — | — |
| N | DNA (5'- D(*AP*CP*CP*TP*TP*AP*TP*TP*TP*GP*CP*AP*TP*AP*C)-3') | dna | 15 | — | — |
| O | DNA (5'- D(*TP*GP*TP*AP*TP*GP*CP*AP*AP*AP*TP*AP*AP*GP*G)-3') | dna | 14 | — | — |
| P | DNA (5'- D(*AP*CP*CP*TP*TP*AP*TP*TP*TP*GP*CP*AP*TP*AP*C)-3') | dna | 14 | — | — |
| A | Pou domain, class 2, transcription factor 1 | protein | 134 | 67% helix, 0% strand | P14859 |
| B | Pou domain, class 2, transcription factor 1 | protein | 129 | 60% helix, 1% strand | P14859 |
| I | Pou domain, class 2, associating factor 1 | protein | 22 | 32% helix, 0% strand | Q16633 |
| J | Pou domain, class 2, associating factor 1 | protein | 23 | 30% helix, 4% strand | Q16633 |
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 380 | 0.62 | 0.78 | 31 | empty |
| 2 | 143 | 0.58 | 0.83 | 19 | empty |
| 3 | 234 | 0.51 | 0.76 | 29 | empty |
| 4 | 147 | 0.49 | 0.78 | 32 | empty |
| 5 | 116 | 0.44 | 0.78 | 20 | empty |
Interfaces
14 interfaces between chains.
- N–A · 988 Ų buried · 18 hydrogen bonds · protein-nucleic
- O–B · 884 Ų buried · 24 hydrogen bonds · protein-nucleic
- M–A · 864 Ų buried · 19 hydrogen bonds · protein-nucleic
- P–B · 769 Ų buried · 26 hydrogen bonds · protein-nucleic
- O–P · 662 Ų buried · 58 hydrogen bonds · nucleic-nucleic
Compared structures
- 1CQT · Crystal structure of a ternary complex containing an oca-B peptide, the oct-1 pou domain… · the same entry in another collection · chain J against J, TM-score 1.00
- P14859 · AlphaFold monomer V2.0 prediction for pou domain, class 2, transcription factor 1 (P14859) · a predicted model of the same protein · chain B against A, TM-score 0.92
- Q16633 · AlphaFold monomer V2.0 prediction for pou domain class 2-associating factor 1 (Q16633) · a predicted model of the same protein · chain J against A, TM-score 0.59
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 P14859
- Every structure of UniProt Q16633
- Elsewhere: RCSB PDB 1CQT · PDBe 1CQT · UniProt P14859 · UniProt Q16633
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