MolNFT v1 · #121210 · protein
Crystal structure of the carboxy-terminal domain of yeast CTF4 bound to DNA2.
5HOG · DNA polymerase alpha-binding protein: “Crystal structure of the carboxy-terminal domain of yeast CTF4 bound to DNA2.”. X-ray diffraction, 19 pockets (best druggability 0.81). MolNFT v1 #121210 on GenesisL1: 3D structure, binding…
- PDB
- 5HOG
- Type
- protein
- Length
- 1,180 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase alpha-binding protein; DNA2P
- UniProt
- Q01454, A0A0D4IHI3
- Pockets
- 19 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 21% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase alpha-binding protein | protein | 425 | 27% helix, 34% strand | Q01454 |
| B | DNA polymerase alpha-binding protein | protein | 432 | 27% helix, 33% strand | Q01454 |
| C | DNA polymerase alpha-binding protein | protein | 296 | 4% helix, 47% strand | Q01454 |
| D | DNA2P | protein | 13 | 31% helix, 0% strand | A0A0D4IHI3 |
| E | DNA2P | protein | 14 | 29% helix, 0% strand | A0A0D4IHI3 |
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 903 | 0.81 | 0.83 | 85 | empty |
| 2 | 73 | 0.68 | 0.94 | 22 | empty |
| 3 | 334 | 0.65 | 0.80 | 44 | empty |
| 4 | 185 | 0.65 | 0.85 | 31 | empty |
| 5 | 277 | 0.64 | 0.81 | 43 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1592 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1590 Ų buried · 19 hydrogen bonds · protein-protein
- B–E · 596 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 585 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 274 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5HOG · Crystal structure of the carboxy-terminal domain of yeast Ctf4 bound to Dna2. · the same entry in another collection · chain E against E, TM-score 1.00
- Q01454 · AlphaFold monomer V2.0 prediction for DNA polymerase alpha-binding protein (Q01454) · a predicted model of the same protein · chain B against A, 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 Q01454
- Every structure of UniProt A0A0D4IHI3
- Elsewhere: RCSB PDB 5HOG · PDBe 5HOG · UniProt Q01454 · UniProt A0A0D4IHI3
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