MolNFT v1 · #21214 · protein + DNA
Molecular recognition of the nucleosomal 'supergroove'
1S32 · Palindromic alpha-satellite 146 bp DNA fragment: “Molecular recognition of the nucleosomal 'supergroove'”. X-ray diffraction, 8 ligands (PYB, IMT, ABU), 20 pockets (best druggability 0.81). MolNFT v1 #21214 on GenesisL1: 3D…
- PDB
- 1S32
- Type
- protein + DNA
- Length
- 1,071 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Palindromic alpha-satellite 146 bp DNA fragment; Histone H3; Histone H4; Histone H2A…
- UniProt
- P02304
- Ligands
- PYB, IMT, ABU, BAL, DIB, OGG, MN, CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 9 distinct chains · 63% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I, J | Palindromic alpha-satellite 146 bp DNA fragment | dna | 146 | — | — |
| A | Histone H3 | protein | 98 | 65% helix, 4% strand | — |
| B | Histone H4 | protein | 81 | 62% helix, 9% strand | P02304 |
| C | Histone H2A | protein | 107 | 56% helix, 7% strand | — |
| D | Histone H2B | protein | 101 | 67% helix, 4% strand | — |
| E | Histone H3 | protein | 99 | 67% helix, 4% strand | — |
| F | Histone H4 | protein | 88 | 57% helix, 8% strand | P02304 |
| G | Histone H2A | protein | 107 | 56% helix, 7% strand | — |
| H | Histone H2B | protein | 98 | 70% helix, 4% strand | — |
Ligands and binding sites
- PYB · 4-amino-(1-methylpyrrole)-2-carboxylic acid · ligand · 12 copies · chains I, J, C, G
- IMT · 4-amino-(1-methylimidazole)-2-carboxylic acid · ligand · 4 copies · chains I, C, J
- ABU · Gamma-amino-butanoic acid · ligand · 2 copies · chains I, J
- BAL · Beta-alanine · ligand · 2 copies · chains I, J, C, G
- DIB · 3-amino-(dimethylpropylamine) · ligand · 2 copies · chains I, J
- OGG · 2-(2-carbamoylmethoxy-ethoxy)-acetamide · ligand · chains I, J
- MN · Manganese (II) ion · metal · 14 copies · chains I, J, E, F
- CL · Chloride ion · ion · 4 copies · chains A, J, C, D, E, I, G, H
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 | 942 | 0.81 | 0.83 | 78 | empty |
| 2 | 471 | 0.76 | 0.85 | 48 | empty |
| 3 | 343 | 0.75 | 0.86 | 46 | empty |
| 4 | 1136 | 0.71 | 0.75 | 76 | empty |
| 5 | 428 | 0.68 | 0.80 | 37 | empty |
Interfaces
36 interfaces between chains.
- I–J · 6386 Ų buried · 521 hydrogen bonds · nucleic-nucleic
- C–D · 2662 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 2635 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 2605 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2561 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 1S32 · Molecular Recognition of the Nucleosomal 'Supergroove' · the same entry in another collection · chain I against I, 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 P02304
- Elsewhere: RCSB PDB 1S32 · PDBe 1S32 · UniProt P02304
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