Research workbench
Crystal structure of the carboxy-terminal domain of yeast CTF4 bound to pol alpha.
Analyse Crystal structure of the carboxy-terminal domain of yeast CTF4 bound to pol… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4C93
- Type
- protein
- Length
- 1,171 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase alpha-binding protein; DNA polymerase alpha catalytic subunit a
- EC
- 2.7.7.7
- UniProt
- Q01454, P13382
- Pockets
- 19 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 36% 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, 32% strand | Q01454 |
| C | DNA polymerase alpha-binding protein | protein | 296 | 6% helix, 47% strand | Q01454 |
| D, E | DNA polymerase alpha catalytic subunit a (EC 2.7.7.7) | protein | 10 | 80% helix, 0% strand | P13382 |
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 | 922 | 0.81 | 0.83 | 87 | empty |
| 2 | 108 | 0.75 | 0.95 | 21 | empty |
| 3 | 249 | 0.68 | 0.84 | 39 | empty |
| 4 | 320 | 0.65 | 0.80 | 46 | empty |
| 5 | 309 | 0.64 | 0.80 | 52 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1570 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1557 Ų buried · 19 hydrogen bonds · protein-protein
- B–E · 617 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 588 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 271 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4C93 · Crystal structure of the carboxy-terminal domain of yeast Ctf4 bound to Pol alpha. · 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
- P13382 · AlphaFold monomer V2.0 prediction for DNA polymerase alpha catalytic subunit a (P13382) · a predicted model of the same protein · chain D against A, TM-score 0.86
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 P13382
- Elsewhere: RCSB PDB 4C93 · PDBe 4C93 · UniProt Q01454 · UniProt P13382
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