Research workbench
Crystal structure of human polymerase eta complexed with syn N7- acetophenoneguanine
Analyse Crystal structure of human polymerase eta complexed with syn N7… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LCD
- Type
- protein + DNA
- Length
- 444 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase eta; DNA (5'-D(*CP*AP*T*(T0P)P*CP*TP*CP*AP*CP*AP*CP*T)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q9Y253
- Ligands
- T0P
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase eta (EC 2.7.7.7) | protein | 427 | 43% helix, 22% strand | Q9Y253 |
| T | DNA (5'-D(*CP*AP*T*(T0P)P*CP*TP*CP*AP*CP*AP*CP*T)-3') | dna | 9 | — | — |
| P | DNA (5'-D(*AP*GP*TP*GP*TP*GP*AP*G)-3') | dna | 8 | — | — |
Ligands and binding sites
- T0P · [(2~{R},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-7-phenacyl-1~{H}-purin-9-yl)-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate · ligand · chains A, T, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1070 | 0.81 | 0.82 | 78 | T0P |
| 2 | 410 | 0.71 | 0.83 | 36 | empty |
| 3 | 201 | 0.67 | 0.86 | 25 | empty |
| 4 | 105 | 0.44 | 0.78 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–T · 839 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–P · 610 Ų buried · 15 hydrogen bonds · protein-nucleic
- T–P · 368 Ų buried · 31 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7LCD · Crystal structure of human polymerase eta complexed with syn N7-acetophe guanine · the same entry in another collection · chain A 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 Q9Y253
- Elsewhere: RCSB PDB 7LCD · PDBe 7LCD · UniProt Q9Y253
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