MolNFT v1 · #128670 · protein
Crystal structure of the carboxy-terminal domain of yeast CTF4 bound to a stapled SLD5 cip
5NXQ · DNA polymerase alpha-binding protein: “Crystal structure of the carboxy-terminal domain of yeast CTF4 bound to a stapled SLD5 cip”. X-ray diffraction, 20 pockets (best druggability 0.81). MolNFT v1 #128670 on GenesisL1: 3D…
- PDB
- 5NXQ
- Type
- protein
- Length
- 1,181 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase alpha-binding protein; Met-asp-ile-UA1-ile-asp-asp-ile-leu-UA2-glu-leu-asp…
- UniProt
- Q01454
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase alpha-binding protein | protein | 424 | 26% helix, 34% strand | Q01454 |
| B | DNA polymerase alpha-binding protein | protein | 431 | 26% helix, 33% strand | Q01454 |
| C | DNA polymerase alpha-binding protein | protein | 296 | 5% helix, 47% strand | Q01454 |
| D, E | Met-asp-ile-UA1-ile-asp-asp-ile-leu-UA2-glu-leu-asp-lys- glu | protein | 15 | 53% helix, 0% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 983 | 0.81 | 0.83 | 90 | empty |
| 2 | 93 | 0.71 | 0.94 | 20 | empty |
| 3 | 303 | 0.64 | 0.80 | 47 | empty |
| 4 | 274 | 0.64 | 0.81 | 40 | empty |
| 5 | 280 | 0.63 | 0.80 | 35 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1588 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1527 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 710 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 710 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 264 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 5NXQ · Crystal structure of the carboxy-terminal domain of yeast Ctf4 bound to a stapled Sld5 CIP · 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
- Elsewhere: RCSB PDB 5NXQ · PDBe 5NXQ · UniProt Q01454
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