Research workbench
Human cst-DNA polymerase ALPHA/PRIMASE preinitiation complex bound to 4XTEL-foldback template - PRIM2C advanced pic
Analyse Human cst-DNA polymerase ALPHA/PRIMASE preinitiation complex bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8D0K
- Type
- protein + DNA
- Length
- 3,840 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cst complex subunit CTC1; Cst complex subunit STN1; Cst complex subunit TEN1; DNA primase…
- EC
- 2.7.7.102, 2.7.7.7
- UniProt
- Q2NKJ3, Q9H668, Q86WV5, P49642, P49643, P09884, Q14181
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 8 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cst complex subunit CTC1 | protein | 1116 | 19% helix, 31% strand | Q2NKJ3 |
| B | Cst complex subunit STN1 | protein | 362 | 41% helix, 20% strand | Q9H668 |
| C | Cst complex subunit TEN1 | protein | 121 | 21% helix, 40% strand | Q86WV5 |
| D | DNA primase small subunit (EC 2.7.7.102) | protein | 419 | 53% helix, 9% strand | P49642 |
| E | DNA primase large subunit | protein | 431 | 59% helix, 3% strand | P49643 |
| F | DNA polymerase alpha catalytic subunit (EC 2.7.7.7) | protein | 915 | 36% helix, 21% strand | P09884 |
| G | DNA polymerase alpha subunit B | protein | 456 | 22% helix, 25% strand | Q14181 |
| H | DNA (5'- D(P*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*A)-3') | dna | 20 | — | — |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 173 | 0.82 | 0.97 | 39 | empty |
| 2 | 1154 | 0.81 | 0.82 | 126 | empty |
| 3 | 156 | 0.78 | 0.94 | 34 | empty |
| 4 | 1029 | 0.77 | 0.79 | 96 | empty |
| 5 | 503 | 0.76 | 0.84 | 71 | empty |
Interfaces
19 interfaces between chains.
- A–B · 1951 Ų buried · 11 hydrogen bonds · protein-protein
- F–G · 1797 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 1497 Ų buried · 19 hydrogen bonds · protein-protein
- A–H · 1233 Ų buried · 20 hydrogen bonds · protein-nucleic
- B–C · 1228 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 8D0K · Human CST-DNA polymerase alpha/primase preinitiation complex bound to 4xTEL-foldback… · the same entry in another collection · chain G against G, TM-score 1.00
- Q14181 · AlphaFold monomer V2.0 prediction for DNA polymerase alpha subunit B (Q14181) · a predicted model of the same protein · chain G against A, TM-score 0.97
- P49642 · AlphaFold monomer V2.0 prediction for DNA primase small subunit (P49642) · a predicted model of the same protein · chain D against A, TM-score 0.97
- Q86WV5 · AlphaFold monomer V2.0 prediction for cst complex subunit TEN1 (Q86WV5) · a predicted model of the same protein · chain C against A, TM-score 0.96
- Q2NKJ3 · AlphaFold monomer V2.0 prediction for cst complex subunit CTC1 (Q2NKJ3) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 Q2NKJ3
- Every structure of UniProt Q9H668
- Every structure of UniProt Q86WV5
- Every structure of UniProt P49642
- Every structure of UniProt P49643
- Every structure of UniProt P09884
- Every structure of UniProt Q14181
- Elsewhere: RCSB PDB 8D0K · PDBe 8D0K · UniProt Q2NKJ3 · UniProt Q9H668 · UniProt Q86WV5 · UniProt P49642 · UniProt P49643 · UniProt P09884 · UniProt Q14181
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