MolNFT v1 · #114386 · protein
Crystal structure of human MCM2 hbd and ASF1B chaperoning a histone H3.3-H4 dimer
5BNX: “Crystal structure of human MCM2 hbd and ASF1B chaperoning a histone H3.3-H4 dimer”. X-ray diffraction, 4 pockets (best druggability 0.66). MolNFT v1 #114386 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5BNX
- Type
- protein
- Length
- 374 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.3; Histone H4; DNA replication licensing factor MCM2; Histone chaperone ASF1B
- UniProt
- P84243, P62805, P49736, Q9NVP2
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.3 | protein | 77 | 69% helix, 4% strand | P84243 |
| B | Histone H4 | protein | 86 | 56% helix, 8% strand | P62805 |
| C | DNA replication licensing factor MCM2 | protein | 57 | 44% helix, 5% strand | P49736 |
| D | Histone chaperone ASF1B | protein | 154 | 12% helix, 53% strand | Q9NVP2 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 531 | 0.66 | 0.77 | 49 | empty |
| 2 | 64 | 0.45 | 0.82 | 18 | empty |
| 3 | 53 | 0.38 | 0.80 | 14 | GOL |
| 4 | 75 | 0.31 | 0.73 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2178 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1242 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 896 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 875 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 585 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5BNX · Crystal structure of Human MCM2 HBD and ASF1b chaperoning a histone H3.3-H4 dimer · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NVP2 · AlphaFold monomer V2.0 prediction for histone chaperone ASF1B (Q9NVP2) · a predicted model of the same protein · chain D against A, 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 0.92
- P49736 · AlphaFold monomer V2.0 prediction for DNA replication licensing factor MCM2 (P49736) · a predicted model of the same protein · chain C against A, TM-score 0.44
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
- Every structure of UniProt Q9NVP2
- Elsewhere: RCSB PDB 5BNX · PDBe 5BNX · UniProt P84243 · UniProt P62805 · UniProt P49736 · UniProt Q9NVP2
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