MolNFT v1 · #81227 · protein + DNA
Crystal structure of RAP1/DNA complex
3UKG · DNA-binding protein RAP1: “Crystal structure of RAP1/DNA complex”. X-ray diffraction, 1 ligand (CA), 5 pockets (best druggability 0.57). MolNFT v1 #81227 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3UKG
- Type
- protein + DNA
- Length
- 285 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-binding protein RAP1; Telomeric DNA
- UniProt
- P11938
- Ligands
- CA
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-binding protein RAP1 | protein | 223 | 41% helix, 3% strand | P11938 |
| C | Telomeric DNA | dna | 31 | — | — |
| D | Telomeric DNA | dna | 31 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 274 | 0.57 | 0.78 | 23 | empty |
| 2 | 119 | 0.55 | 0.83 | 23 | empty |
| 3 | 133 | 0.47 | 0.79 | 15 | empty |
| 4 | 120 | 0.41 | 0.76 | 17 | empty |
| 5 | 52 | 0.23 | 0.72 | 12 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1363 Ų buried · 129 hydrogen bonds · nucleic-nucleic
- A–C · 1330 Ų buried · 40 hydrogen bonds · protein-nucleic
- A–D · 1221 Ų buried · 35 hydrogen bonds · protein-nucleic
Compared structures
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 P11938
- Elsewhere: RCSB PDB 3UKG · PDBe 3UKG · UniProt P11938
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