MolNFT v1 · #14185 · protein + DNA
Ligand binding alters the structure and dynamics of nucleosomal DNA
1M18 · Palindromic 146 base pair DNA fragment: “Ligand binding alters the structure and dynamics of nucleosomal DNA”. X-ray diffraction, 2 ligands (1SZ, MN), 20 pockets (best druggability 0.77). MolNFT v1 #14185 on GenesisL1: 3D structure…
- PDB
- 1M18
- Type
- protein + DNA
- Length
- 1,052 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Palindromic 146 base pair DNA fragment; Histone H3.2; Histone H4; Histone H2A.1; Histone…
- UniProt
- P02302, P02304, P06897, P02281
- Ligands
- 1SZ, MN
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 8 distinct chains · 62% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I, J | Palindromic 146 base pair DNA fragment | dna | 146 | — | — |
| A | Histone H3.2 | protein | 98 | 65% helix, 4% strand | P02302 |
| B | Histone H4 | protein | 79 | 62% helix, 9% strand | P02304 |
| C | Histone H2A.1 | protein | 107 | 56% helix, 7% strand | P06897 |
| D, H | Histone H2B.1 | protein | 94 | 74% helix, 4% strand | P02281 |
| E | Histone H3.2 | protein | 99 | 65% helix, 4% strand | P02302 |
| F | Histone H4 | protein | 83 | 60% helix, 8% strand | P02304 |
| G | Histone H2A.1 | protein | 106 | 56% helix, 7% strand | P06897 |
Ligands and binding sites
- 1SZ · N-[5-[[4-[[5-[[5-[[5-[[5-[[3-[3-(dimethylamino)propylamino]-3-oxidanylidene-propyl]carbamoyl]-1-methyl-pyrrol-3-yl]carbamoyl]-1-methyl-pyrrol-3-yl]carbamoyl]-1-methyl-pyrrol-3-yl]carbamoyl]-1-methyl-pyrrol-3-yl]amino]-4-oxidanylidene-butyl]carbamoyl]-1-methyl-pyrrol-3-yl]-1-methyl-4-[[1-methyl-4-[(1-methylimidazol-2-yl)carbonylamino]pyrrol-2-yl]carbonylamino]imidazole-2-carboxamide · ligand · 2 copies · chains I, J, G, C
- MN · Manganese (II) ion · metal · 11 copies · chains I, J, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 643 | 0.77 | 0.83 | 65 | empty |
| 2 | 432 | 0.76 | 0.86 | 62 | empty |
| 3 | 481 | 0.74 | 0.83 | 49 | empty |
| 4 | 378 | 0.72 | 0.83 | 55 | empty |
| 5 | 766 | 0.70 | 0.77 | 55 | empty |
Interfaces
36 interfaces between chains.
- I–J · 6297 Ų buried · 482 hydrogen bonds · nucleic-nucleic
- C–D · 2665 Ų buried · 22 hydrogen bonds · protein-protein
- G–H · 2632 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 2598 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2522 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
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 P02302
- Every structure of UniProt P02304
- Every structure of UniProt P06897
- Every structure of UniProt P02281
- Elsewhere: RCSB PDB 1M18 · PDBe 1M18 · UniProt P02302 · UniProt P02304 · UniProt P06897 · UniProt P02281
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