MolNFT v1 · #159328 · protein + DNA
Crystal structure of the ORC1 bah domain in complex with a nucleosome core particle
6OM3 · Histone H3.2: “Crystal structure of the ORC1 bah domain in complex with a nucleosome core particle”. X-ray diffraction, 1 ligand (ACE), 20 pockets (best druggability 0.78). MolNFT v1 #159328 on GenesisL1: 3D structure, binding sites…
- PDB
- 6OM3
- Type
- protein + DNA
- Length
- 2,778 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.2; Histone H4; Histone H2A; Histone H2B 1.1; DNA (146-mer); DNA (147-mer)…
- UniProt
- P84233, P62799, Q6AZJ8, P02281, P54784
- Ligands
- ACE
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 15 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.2 | protein | 97 | 63% helix, 4% strand | P84233 |
| B, N | Histone H4 | protein | 84 | 60% helix, 8% strand | P62799 |
| C | Histone H2A | protein | 104 | 57% helix, 6% strand | Q6AZJ8 |
| D, H, P, T | Histone H2B 1.1 | protein | 93 | 74% helix, 4% strand | P02281 |
| E, Q | Histone H3.2 | protein | 95 | 67% helix, 4% strand | P84233 |
| F | Histone H4 | protein | 83 | 61% helix, 7% strand | P62799 |
| G, O, S | Histone H2A | protein | 107 | 53% helix, 7% strand | Q6AZJ8 |
| I, U | DNA (146-mer) | dna | 146 | — | — |
| J, V | DNA (147-mer) | dna | 147 | — | — |
| K | Origin recognition complex subunit 1 | protein | 177 | 19% helix, 39% strand | P54784 |
| L | Origin recognition complex subunit 1 | protein | 198 | 24% helix, 34% strand | P54784 |
| M | Histone H3.2 | protein | 98 | 63% helix, 4% strand | P84233 |
| R | Histone H4 | protein | 80 | 64% helix, 9% strand | P62799 |
| W | Origin recognition complex subunit 1 | protein | 195 | 23% helix, 34% strand | P54784 |
| X | Origin recognition complex subunit 1 | protein | 109 | 19% helix, 30% strand | P54784 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 4 copies · chains K, L, W, X
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 | 636 | 0.78 | 0.83 | 69 | empty |
| 2 | 413 | 0.76 | 0.86 | 42 | empty |
| 3 | 590 | 0.76 | 0.82 | 69 | empty |
| 4 | 444 | 0.75 | 0.84 | 49 | empty |
| 5 | 486 | 0.75 | 0.83 | 59 | empty |
Interfaces
84 interfaces between chains.
- I–J · 6560 Ų buried · 506 hydrogen bonds · nucleic-nucleic
- U–V · 6496 Ų buried · 506 hydrogen bonds · nucleic-nucleic
- A–B · 2656 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 2641 Ų buried · 24 hydrogen bonds · protein-protein
- O–P · 2607 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6OM3 · Crystal structure of the Orc1 BAH domain in complex with a nucleosome core particle · 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 Q6AZJ8
- Every structure of UniProt P02281
- Every structure of UniProt P54784
- Elsewhere: RCSB PDB 6OM3 · PDBe 6OM3 · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281 · UniProt P54784
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