Research workbench
Archaeal DNA ligase and heterotrimeric PCNA in complex with adenylated DNA
Analyse Archaeal DNA ligase and heterotrimeric PCNA in complex with adenylated DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RPW
- Type
- protein + DNA
- Length
- 1,241 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase sliding clamp 1; DNA polymerase sliding clamp 2; DNA polymerase sliding…
- EC
- 6.5.1.1
- UniProt
- P57766, Q97Z84, P57765, Q980T8
- Ligands
- AMP, MN
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 7 distinct chains · 23% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase sliding clamp 1 | protein | 252 | 15% helix, 34% strand | P57766 |
| B | DNA polymerase sliding clamp 2 | protein | 243 | 14% helix, 31% strand | Q97Z84 |
| C | DNA polymerase sliding clamp 3 | protein | 245 | 12% helix, 30% strand | P57765 |
| X | Upstream strand DNA | dna | 20 | — | — |
| Y | Downstream strand DNA | dna | 11 | — | — |
| Z | Template strand DNA | dna | 31 | — | — |
| E | DNA ligase (EC 6.5.1.1) | protein | 439 | 39% helix, 10% strand | Q980T8 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains Y, E
- MN · Manganese (II) ion · metal · 4 copies · chains X, E, Y
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 | 262 | 0.84 | 0.95 | 40 | empty |
| 2 | 318 | 0.82 | 0.92 | 51 | MN |
| 3 | 177 | 0.81 | 0.95 | 31 | empty |
| 4 | 135 | 0.80 | 0.96 | 31 | empty |
| 5 | 95 | 0.78 | 0.98 | 38 | empty |
Interfaces
16 interfaces between chains.
- C–E · 1057 Ų buried · 3 hydrogen bonds · protein-protein
- X–Z · 916 Ų buried · 66 hydrogen bonds · nucleic-nucleic
- B–C · 795 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 793 Ų buried · 9 hydrogen bonds · protein-protein
- Z–E · 687 Ų buried · 20 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7RPW · Archaeal DNA ligase and heterotrimeric PCNA in complex with adenylated DNA · the same entry in another collection · chain E against E, TM-score 1.00
- Q97Z84 · AlphaFold monomer V2.0 prediction for DNA polymerase sliding clamp 2 (Q97Z84) · a predicted model of the same protein · chain B against A, TM-score 0.95
- P57766 · AlphaFold monomer V2.0 prediction for DNA polymerase sliding clamp 1 (P57766) · a predicted model of the same protein · chain A against A, TM-score 0.93
- P57765 · AlphaFold monomer V2.0 prediction for DNA polymerase sliding clamp 3 (P57765) · a predicted model of the same protein · chain C against A, TM-score 0.93
- Q980T8 · AlphaFold monomer V2.0 prediction for DNA ligase (Q980T8) · a predicted model of the same protein · chain E against A, TM-score 0.89
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 P57766
- Every structure of UniProt Q97Z84
- Every structure of UniProt P57765
- Every structure of UniProt Q980T8
- Elsewhere: RCSB PDB 7RPW · PDBe 7RPW · UniProt P57766 · UniProt Q97Z84 · UniProt P57765 · UniProt Q980T8
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