MolNFT v1 · #114384 · protein
Crystal structure of human MCM2 hbd chaperoning a histone H3-H4 tetramer
5BNV · Histone H3.3: “Crystal structure of human MCM2 hbd chaperoning a histone H3-H4 tetramer”. X-ray diffraction, 1 ligand (PO4), 2 pockets (best druggability 0.35). MolNFT v1 #114384 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5BNV
- Type
- protein
- Length
- 418 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.3; Histone H4; DNA replication licensing factor MCM2
- UniProt
- P84243, P62805, P49736
- Ligands
- PO4
- Pockets
- 2 · best druggability 0.35
Structure
x-ray diffraction · 6 distinct chains · 59% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.3 | protein | 77 | 68% helix, 5% strand | P84243 |
| B | Histone H4 | protein | 79 | 65% helix, 5% strand | P62805 |
| D | Histone H3.3 | protein | 78 | 68% helix, 4% strand | P84243 |
| E | Histone H4 | protein | 69 | 67% helix, 6% strand | P62805 |
| F | DNA replication licensing factor MCM2 | protein | 58 | 36% helix, 5% strand | P49736 |
| C | DNA replication licensing factor MCM2 | protein | 57 | 42% helix, 5% strand | P49736 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 3 copies · chains B, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.35 | 0.78 | 13 | empty |
| 2 | 58 | 0.27 | 0.74 | 15 | empty |
Interfaces
7 interfaces between chains.
- A–B · 2112 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1906 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1433 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 1155 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 880 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5BNV · Crystal structure of Human MCM2 HBD chaperoning a histone H3-H4 tetramer · the same entry in another collection · chain C against C, TM-score 1.00
- P84243 · AlphaFold monomer V2.0 prediction for histone H3.3 (P84243) · a predicted model of the same protein · chain A against A, TM-score 0.97
- P49736 · AlphaFold monomer V2.0 prediction for DNA replication licensing factor MCM2 (P49736) · a predicted model of the same protein · chain F against A, TM-score 0.46
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 P84243
- Every structure of UniProt P62805
- Every structure of UniProt P49736
- Elsewhere: RCSB PDB 5BNV · PDBe 5BNV · UniProt P84243 · UniProt P62805 · UniProt P49736
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