MolNFT v1 · #63835 · protein
Crystal structure of the carboxyl-terminal domain of yeast DNA polymerase alpha in complex with its B subunit
3FLO · DNA polymerase alpha subunit B: “Crystal structure of the carboxyl-terminal domain of yeast DNA polymerase alpha in complex with its B subunit”. X-ray diffraction, 2 ligands (ZN, SO4), 20 pockets (best druggability 0.78). MolNFT v1…
- PDB
- 3FLO
- Type
- protein
- Length
- 2,464 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase alpha subunit B; DNA polymerase alpha catalytic subunit a
- EC
- 2.7.7.7
- UniProt
- P38121, P13382
- Ligands
- ZN, SO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | DNA polymerase alpha subunit B | protein | 433 | 25% helix, 27% strand | P38121 |
| I, J, K, L | DNA polymerase alpha catalytic subunit a | protein | 3 | 0% helix, 33% strand | — |
| B, D, F, H | DNA polymerase alpha catalytic subunit a (EC 2.7.7.7) | protein | 180 | 36% helix, 15% strand | P13382 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains B, D, F, H
- SO4 · Sulfate ion · ion · 65 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 679 | 0.78 | 0.83 | 53 | SO4 |
| 2 | 503 | 0.74 | 0.83 | 64 | SO4 |
| 3 | 511 | 0.74 | 0.82 | 69 | SO4 |
| 4 | 856 | 0.72 | 0.77 | 90 | empty |
| 5 | 239 | 0.71 | 0.87 | 36 | SO4 |
Interfaces
17 interfaces between chains.
- G–H · 2335 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2333 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 2322 Ų buried · 31 hydrogen bonds · protein-protein
- E–F · 2320 Ų buried · 36 hydrogen bonds · protein-protein
- A–G · 569 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3FLO · Crystal structure of the carboxyl-terminal domain of yeast DNA polymerase alpha in… · the same entry in another collection · chain H against H, 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 P38121
- Every structure of UniProt P13382
- Elsewhere: RCSB PDB 3FLO · PDBe 3FLO · UniProt P38121 · UniProt P13382
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