MolNFT v1 · #124477 · protein + DNA
Structural model of 53BP1 bound to a ubiquitylated and methylated nucleosome, at 4.5 a resolution
5KGF · Histone H3.2: “Structural model of 53BP1 bound to a ubiquitylated and methylated nucleosome, at 4.5 a resolution”. Electron microscopy, 20 pockets (best druggability 0.78). MolNFT v1 #124477 on GenesisL1: 3D structure, binding sites…
- PDB
- 5KGF
- Type
- protein + DNA
- Length
- 1,276 residues
- Chains
- 14
- 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; DNA…
- UniProt
- P84233, P62799, P0C0S8, P62807, H7BZY0, P0CG47
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 10 distinct chains · 59% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.2 | protein | 101 | 65% helix, 3% strand | P84233 |
| B, F | Histone H4 | protein | 84 | 61% helix, 5% strand | P62799 |
| C, G | Histone H2A type 1 | protein | 113 | 55% helix, 4% strand | P0C0S8 |
| D | Histone H2B type 1-C/E/F/G/I | protein | 100 | 70% helix, 4% strand | P62807 |
| E | Histone H3.2 | protein | 100 | 66% helix, 3% strand | P84233 |
| H | Histone H2B type 1-C/E/F/G/I | protein | 97 | 72% helix, 3% strand | P62807 |
| I | DNA (145-mer) | dna | 145 | — | — |
| J | DNA (145-mer) | dna | 145 | — | — |
| L, K | Tumor suppressor P53-binding protein 1 | protein | 21 | 29% helix, 0% strand | H7BZY0 |
| O, M | Ubiquitin | protein | 76 | 20% helix, 30% strand | P0CG47 |
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 | 477 | 0.78 | 0.86 | 55 | empty |
| 2 | 1158 | 0.76 | 0.79 | 104 | empty |
| 3 | 244 | 0.75 | 0.89 | 46 | empty |
| 4 | 263 | 0.74 | 0.88 | 47 | empty |
| 5 | 274 | 0.71 | 0.86 | 41 | empty |
Interfaces
52 interfaces between chains.
- I–J · 6584 Ų buried · 699 hydrogen bonds · nucleic-nucleic
- C–D · 2582 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2500 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 2466 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 2466 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 5KGF · Structural model of 53BP1 bound to a ubiquitylated and methylated nucleosome, at 4.5 A… · the same entry in another collection · chain K against K, 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 P84233
- Every structure of UniProt P62799
- Every structure of UniProt P0C0S8
- Every structure of UniProt P62807
- Every structure of UniProt H7BZY0
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 5KGF · PDBe 5KGF · UniProt P84233 · UniProt P62799 · UniProt P0C0S8 · UniProt P62807 · UniProt H7BZY0 · UniProt P0CG47
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