MolNFT v1 · #141552 · protein
Crystal structure of RTT109-ASF1-H3-H4 complex
5ZBB · DNA damage response protein RTT109, putative: “Crystal structure of RTT109-ASF1-H3-H4 complex”. X-ray diffraction, 1 ligand (IOD), 10 pockets (best druggability 0.70). MolNFT v1 #141552 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5ZBB
- Type
- protein
- Length
- 689 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA damage response protein RTT109, putative; Histone chaperone ASF1; Histone H3; Histone…
- UniProt
- Q4WUS9, Q4WXX5, P61830, P02309
- Ligands
- IOD
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA damage response protein RTT109, putative | protein | 361 | 31% helix, 24% strand | Q4WUS9 |
| B | Histone chaperone ASF1 | protein | 154 | 7% helix, 51% strand | Q4WXX5 |
| C | Histone H3 | protein | 92 | 58% helix, 7% strand | P61830 |
| D | Histone H4 | protein | 82 | 62% helix, 10% strand | P02309 |
Ligands and binding sites
- IOD · Iodide ion · ion · 23 copies · chains A, C, D, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 430 | 0.70 | 0.81 | 52 | IOD |
| 2 | 210 | 0.69 | 0.86 | 29 | IOD |
| 3 | 279 | 0.68 | 0.83 | 40 | IOD, PEG |
| 4 | 415 | 0.65 | 0.78 | 47 | IOD |
| 5 | 187 | 0.58 | 0.81 | 25 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2613 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1152 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 935 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 651 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 548 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide, 1 modified (disulfide, acetylation).
Compared structures
- 5ZBB · Crystal structure of Rtt109-Asf1-H3-H4 complex · the same entry in another collection · chain C against C, TM-score 1.00
- Q4WXX5 · AlphaFold monomer V2.0 prediction for histone chaperone ASF1 (Q4WXX5) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P61830 · AlphaFold monomer V2.0 prediction for histone H3 (P61830) · a predicted model of the same protein · chain C against A, TM-score 0.84
- P02309 · AlphaFold monomer V2.0 prediction for histone H4 (P02309) · a predicted model of the same protein · chain D against A, TM-score 0.82
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 Q4WUS9
- Every structure of UniProt Q4WXX5
- Every structure of UniProt P61830
- Every structure of UniProt P02309
- Elsewhere: RCSB PDB 5ZBB · PDBe 5ZBB · UniProt Q4WUS9 · UniProt Q4WXX5 · UniProt P61830 · UniProt P02309
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