MolNFT v1 · #167173 · protein + DNA
Sra domain of UHRF1 in complex with DNA
6VCS · E3 ubiquitin-protein ligase UHRF1: “Sra domain of UHRF1 in complex with DNA”. X-ray diffraction, 1 ligand (UNX), 7 pockets (best druggability 0.76). MolNFT v1 #167173 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6VCS
- Type
- protein + DNA
- Length
- 591 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase UHRF1; DNA (5'-D(*GP*CP*CP*TP*GP*TP*AP*CP*AP*GP*GP*C)-3')…
- UniProt
- Q96T88
- Ligands
- UNX
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 18% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase UHRF1 | protein | 187 | 17% helix, 28% strand | Q96T88 |
| B | E3 ubiquitin-protein ligase UHRF1 | protein | 191 | 19% helix, 28% strand | Q96T88 |
| C, D | DNA (5'-D(*GP*CP*CP*TP*GP*TP*AP*CP*AP*GP*GP*C)-3') | dna | 12 | — | — |
| E | E3 ubiquitin-protein ligase UHRF1 | protein | 183 | 17% helix, 30% strand | Q96T88 |
| G | Unk-unk-unk-unk | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- UNX · Unknown atom or ion · ion · 66 copies · chains A, E, C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 976 | 0.76 | 0.79 | 63 | UNX |
| 2 | 249 | 0.62 | 0.81 | 41 | UNX |
| 3 | 111 | 0.57 | 0.85 | 29 | UNX |
| 4 | 118 | 0.50 | 0.81 | 27 | UNX |
| 5 | 158 | 0.49 | 0.78 | 25 | UNX |
Interfaces
11 interfaces between chains.
- C–D · 483 Ų buried · 45 hydrogen bonds · nucleic-nucleic
- B–D · 356 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–C · 352 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–E · 316 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 236 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 6VCS · SRA domain of UHRF1 in complex with DNA · 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 Q96T88
- Elsewhere: RCSB PDB 6VCS · PDBe 6VCS · UniProt Q96T88
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