MolNFT v1 · #166523 · protein + DNA
Structure of two nucleosomes bridged by human PARP2
6USJ · Widom 601 DNA (160-mer): “Structure of two nucleosomes bridged by human PARP2”. Electron microscopy, 20 pockets (best druggability 0.82). MolNFT v1 #166523 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6USJ
- Type
- protein + DNA
- Length
- 2,373 residues
- Chains
- 22
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Widom 601 DNA (160-mer); Histone H3.1; Histone H4; Histone H2A; Histone H2B type 1-J…
- EC
- 2.4.2.30, 2.4.2.-
- UniProt
- P68431, P62805, Q08AJ9, P06899, Q9UGN5
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 14 distinct chains · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I | Widom 601 DNA (160-mer) | dna | 160 | — | — |
| J | Widom 601 DNA (160-mer) | dna | 160 | — | — |
| A, K | Histone H3.1 | protein | 96 | 69% helix, 4% strand | P68431 |
| B, L | Histone H4 | protein | 77 | 64% helix, 8% strand | P62805 |
| C, M | Histone H2A | protein | 108 | 56% helix, 6% strand | Q08AJ9 |
| D, N | Histone H2B type 1-J | protein | 92 | 75% helix, 4% strand | P06899 |
| E, O | Histone H3.1 | protein | 99 | 67% helix, 4% strand | P68431 |
| F, P | Histone H4 | protein | 87 | 54% helix, 7% strand | P62805 |
| G, Q | Histone H2A | protein | 104 | 56% helix, 6% strand | Q08AJ9 |
| H, R | Histone H2B type 1-J | protein | 91 | 76% helix, 4% strand | P06899 |
| S | Widom 601 DNA (160-mer) | dna | 159 | — | — |
| T | Widom 601 DNA (160-mer) | dna | 159 | — | — |
| U | Poly [ADP-ribose] polymerase 2 (EC 2.4.2.30, 2.4.2.-) | protein | 114 | 14% helix, 40% strand | Q9UGN5 |
| V | Poly [ADP-ribose] polymerase 2 (EC 2.4.2.30, 2.4.2.-) | protein | 113 | 23% helix, 38% strand | Q9UGN5 |
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 | 944 | 0.82 | 0.83 | 93 | empty |
| 2 | 449 | 0.75 | 0.84 | 49 | empty |
| 3 | 450 | 0.74 | 0.84 | 49 | empty |
| 4 | 296 | 0.73 | 0.86 | 41 | empty |
| 5 | 337 | 0.72 | 0.85 | 40 | empty |
Interfaces
85 interfaces between chains.
- I–J · 7293 Ų buried · 699 hydrogen bonds · nucleic-nucleic
- S–T · 7256 Ų buried · 702 hydrogen bonds · nucleic-nucleic
- O–P · 2680 Ų buried · 29 hydrogen bonds · protein-protein
- E–F · 2679 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2599 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 6USJ · Structure of two nucleosomes bridged by human PARP2 · the same entry in another collection · chain S against S, 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 P68431
- Every structure of UniProt P62805
- Every structure of UniProt Q08AJ9
- Every structure of UniProt P06899
- Every structure of UniProt Q9UGN5
- Elsewhere: RCSB PDB 6USJ · PDBe 6USJ · UniProt P68431 · UniProt P62805 · UniProt Q08AJ9 · UniProt P06899 · UniProt Q9UGN5
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