Research workbench
Structure of HAP1-PC7 complexed to the uas of CYC7
Analyse Structure of HAP1-PC7 complexed to the uas of CYC7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QP9
- Type
- protein + DNA
- Length
- 373 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*AP*CP*GP*CP*TP*AP*TP*TP*AP*TP*CP*GP*CP*TP*AP*TP*TP*AP*GP*T)-3'); DNA (5'…
- UniProt
- P12351
- Ligands
- ZN
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 7 distinct chains · 56% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, G | DNA (5'- D(*AP*CP*GP*CP*TP*AP*TP*TP*AP*TP*CP*GP*CP*TP*AP*TP*TP*AP*GP*T)-3') | dna | 20 | — | — |
| F | DNA (5'- D(*AP*CP*TP*AP*AP*TP*AP*GP*CP*GP*AP*TP*AP*AP*TP*AP*GP*CP*GP*T)-3') | dna | 20 | — | — |
| H | DNA (5'- D(*AP*CP*TP*AP*AP*TP*AP*GP*CP*GP*AP*TP*AP*AP*TP*AP*GP*CP*GP*T)-3') | dna | 17 | — | — |
| A | CYP1(HAP1-PC7) activatory protein | protein | 76 | 55% helix, 0% strand | P12351 |
| B | CYP1(HAP1-PC7) activatory protein | protein | 74 | 55% helix, 3% strand | P12351 |
| C | CYP1(HAP1-PC7) activatory protein | protein | 71 | 59% helix, 0% strand | P12351 |
| D | CYP1(HAP1-PC7) activatory protein | protein | 75 | 56% helix, 0% strand | P12351 |
Ligands and binding sites
- ZN · Zinc ion · metal · 9 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 768 | 0.79 | 0.83 | 89 | empty |
| 2 | 255 | 0.64 | 0.82 | 28 | empty |
| 3 | 348 | 0.58 | 0.76 | 46 | empty |
| 4 | 183 | 0.56 | 0.80 | 27 | empty |
| 5 | 88 | 0.55 | 0.86 | 14 | empty |
Interfaces
19 interfaces between chains.
- C–D · 1229 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1108 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 937 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 922 Ų buried · 68 hydrogen bonds · nucleic-nucleic
- G–H · 888 Ų buried · 66 hydrogen bonds · nucleic-nucleic
Compared structures
- 1QP9 · Structure of HAP1-PC7 complexed to the uas of CYC7 · the same entry in another collection · chain E against E, 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 P12351
- Elsewhere: RCSB PDB 1QP9 · PDBe 1QP9 · UniProt P12351
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