Research workbench
Structure of VRK1 C-terminal tail bound to nucleosome core particle
Analyse Structure of VRK1 C-terminal tail bound to nucleosome core particle in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TAN
- Type
- protein + DNA
- Length
- 1,062 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.2; Histone H4; Histone H2A type 1; Histone H2B type 1-C/E/F/G/I; Widom 601 DNA…
- EC
- 2.7.11.1
- UniProt
- Q71DI3, P62805, P0C0S8, P62807, Q99986
- Pockets
- 20 · best druggability 0.75
Structure
electron microscopy · 9 distinct chains · 62% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.2 | protein | 98 | 65% helix, 4% strand | Q71DI3 |
| B | Histone H4 | protein | 81 | 63% helix, 9% strand | P62805 |
| C, G | Histone H2A type 1 | protein | 108 | 48% helix, 6% strand | P0C0S8 |
| D, H | Histone H2B type 1-C/E/F/G/I | protein | 93 | 74% helix, 4% strand | P62807 |
| E | Histone H3.2 | protein | 97 | 65% helix, 4% strand | Q71DI3 |
| F | Histone H4 | protein | 82 | 60% helix, 9% strand | P62805 |
| I | Widom 601 DNA (185-mer) | dna | 147 | — | — |
| J | Widom 601 DNA (185-mer) | dna | 147 | — | — |
| K, L | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 4 | 0% helix, 0% strand | Q99986 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1015 | 0.75 | 0.78 | 84 | empty |
| 2 | 563 | 0.73 | 0.81 | 51 | empty |
| 3 | 282 | 0.71 | 0.86 | 31 | empty |
| 4 | 315 | 0.70 | 0.84 | 33 | empty |
| 5 | 557 | 0.69 | 0.79 | 49 | empty |
Interfaces
38 interfaces between chains.
- I–J · 6487 Ų buried · 374 hydrogen bonds · nucleic-nucleic
- C–D · 2627 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 2606 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 2592 Ų buried · 15 hydrogen bonds · protein-protein
- G–H · 2589 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 7TAN · Structure of VRK1 C-terminal tail bound to nucleosome core particle · the same entry in another collection · chain L against L, 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 Q71DI3
- Every structure of UniProt P62805
- Every structure of UniProt P0C0S8
- Every structure of UniProt P62807
- Every structure of UniProt Q99986
- Elsewhere: RCSB PDB 7TAN · PDBe 7TAN · UniProt Q71DI3 · UniProt P62805 · UniProt P0C0S8 · UniProt P62807 · UniProt Q99986
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