Research workbench
The crystal structure of se-ASFVPOLX(L52/163M mutant) in complex with 1NT-gap DNA1
Analyse The crystal structure of se-ASFVPOLX(L52/163M mutant) in complex with 1NT-gap… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HR9
- Type
- protein + DNA
- Length
- 409 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase beta-like protein; DNA (5'-D(*GP*GP*AP*CP*AP*AP*CP*GP*GP*GP*AP*CP*AP*AP*C)…
- UniProt
- A0A0A1E3N6
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase beta-like protein | protein | 176 | 34% helix, 33% strand | A0A0A1E3N6 |
| B | DNA polymerase beta-like protein | protein | 175 | 34% helix, 31% strand | A0A0A1E3N6 |
| C, F | DNA (5'-D(*GP*GP*AP*CP*AP*AP*CP*GP*GP*GP*AP*CP*AP*AP*C)- 3') | dna | 15 | — | — |
| D, E, G, H | DNA (5'-D(*GP*TP*TP*GP*TP*CP*C)-3') | dna | 7 | — | — |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 589 | 0.65 | 0.76 | 52 | empty |
| 2 | 127 | 0.40 | 0.75 | 19 | empty |
| 3 | 50 | 0.28 | 0.76 | 12 | empty |
Interfaces
10 interfaces between chains.
- A–D · 587 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–G · 583 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–B · 377 Ų buried · 2 hydrogen bonds · protein-protein
- B–F · 350 Ų buried · 10 hydrogen bonds · protein-nucleic
- C–D · 345 Ų buried · 24 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 5HR9 · The crystal structure of Se-AsfvPolX(L52/163M mutant) in complex with 1nt-gap DNA1 · 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 A0A0A1E3N6
- Elsewhere: RCSB PDB 5HR9 · PDBe 5HR9 · UniProt A0A0A1E3N6
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