MolNFT v1 · #181782 · protein + DNA
Crystal structure of the hmg-C1 domain of human capicua bound to DNA
7M5W · Protein capicua homolog: “Crystal structure of the hmg-C1 domain of human capicua bound to DNA”. X-ray diffraction, 1 ligand (CA), 3 pockets (best druggability 0.61). MolNFT v1 #181782 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7M5W
- Type
- protein + DNA
- Length
- 174 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein capicua homolog; DNA (5'- D(*GP*GP*TP*TP*AP*TP*GP*AP*AP*TP*GP*AP*AP*AP*AP*AP*GP*C)…
- UniProt
- Q96RK0
- Ligands
- CA
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein capicua homolog | protein | 138 | 72% helix, 0% strand | Q96RK0 |
| B | DNA (5'- D(*GP*GP*TP*TP*AP*TP*GP*AP*AP*TP*GP*AP*AP*AP*AP*AP*GP*C)-3') | dna | 18 | — | — |
| C | DNA (5'- D(*GP*CP*TP*TP*TP*TP*TP*CP*AP*TP*TP*CP*AP*TP*AP*AP*CP*C)-3') | dna | 18 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 390 | 0.61 | 0.77 | 34 | empty |
| 2 | 125 | 0.43 | 0.77 | 24 | empty |
| 3 | 97 | 0.33 | 0.73 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–C · 992 Ų buried · 26 hydrogen bonds · protein-nucleic
- A–B · 957 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–C · 770 Ų buried · 73 hydrogen bonds · nucleic-nucleic
Compared structures
- 7M5W · Crystal structure of the HMG-C1 domain of human capicua bound to DNA · the same entry in another collection · chain A against A, TM-score 1.00
- Q96RK0 · AlphaFold monomer V2.0 prediction for protein capicua homolog (Q96RK0) · a predicted model of the same protein · chain A against A, TM-score 0.57
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 Q96RK0
- Elsewhere: RCSB PDB 7M5W · PDBe 7M5W · UniProt Q96RK0
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