MolNFT v1 · #190762 · protein + DNA
Cryo-EM structure of GAMMAH2AXK15UB-H4K20ME2 nucleosome bound to 53BP1
7YQK · Histone H3.1: “Cryo-EM structure of GAMMAH2AXK15UB-H4K20ME2 nucleosome bound to 53BP1”. Electron microscopy, 20 pockets (best druggability 0.79). MolNFT v1 #190762 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7YQK
- Type
- protein + DNA
- Length
- 1,277 residues
- Chains
- 13
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.1; Histone H4; Histone H2AX; Histone H2B; DNA (145-mer); Polyubiquitin-B; Udr…
- UniProt
- P68431, A0A672PXK1, A0A6P5QZC6, Q2M2T1, J3QS39, A6NNK5
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 13 distinct chains · 49% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.1 | protein | 99 | 61% helix, 4% strand | P68431 |
| B | Histone H4 | protein | 81 | 57% helix, 9% strand | A0A672PXK1 |
| C | Histone H2AX | protein | 112 | 48% helix, 6% strand | A0A6P5QZC6 |
| D | Histone H2B | protein | 96 | 72% helix, 4% strand | Q2M2T1 |
| E | Histone H3.1 | protein | 99 | 62% helix, 3% strand | P68431 |
| F | Histone H4 | protein | 83 | 55% helix, 7% strand | A0A672PXK1 |
| G | Histone H2AX | protein | 111 | 49% helix, 6% strand | A0A6P5QZC6 |
| H | Histone H2B | protein | 95 | 73% helix, 4% strand | Q2M2T1 |
| I | DNA (145-mer) | dna | 145 | — | — |
| J | DNA (145-mer) | dna | 145 | — | — |
| O | Polyubiquitin-B | protein | 75 | 20% helix, 25% strand | J3QS39 |
| K | Udr motif of 53BP1 | protein | 18 | 0% helix, 0% strand | — |
| N | TP53-binding protein 1 | protein | 118 | 9% helix, 43% strand | A6NNK5 |
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1074 | 0.79 | 0.80 | 86 | empty |
| 2 | 241 | 0.74 | 0.89 | 32 | empty |
| 3 | 1097 | 0.73 | 0.77 | 101 | empty |
| 4 | 225 | 0.73 | 0.89 | 33 | empty |
| 5 | 781 | 0.73 | 0.79 | 81 | empty |
Interfaces
43 interfaces between chains.
- I–J · 6481 Ų buried · 551 hydrogen bonds · nucleic-nucleic
- G–H · 2640 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 2548 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 2537 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 2435 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 7YQK · cryo-EM structure of gammaH2AXK15ub-H4K20me2 nucleosome bound to 53BP1 · the same entry in another collection · chain N against N, 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 A0A672PXK1
- Every structure of UniProt A0A6P5QZC6
- Every structure of UniProt Q2M2T1
- Every structure of UniProt J3QS39
- Every structure of UniProt A6NNK5
- Elsewhere: RCSB PDB 7YQK · PDBe 7YQK · UniProt P68431 · UniProt A0A672PXK1 · UniProt A0A6P5QZC6 · UniProt Q2M2T1 · UniProt J3QS39 · UniProt A6NNK5
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