Research workbench
Crystal structures of two intermediates in the assembly of the papillomavirus replication initiation complex
Analyse Crystal structures of two intermediates in the assembly of the papillomavirus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KSY
- Type
- protein + DNA
- Length
- 501 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E1 recognition sequence, strand 1; E1 recognition sequence, strand 2; Replication protein…
- UniProt
- P03116
- Pockets
- 7 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, E | E1 recognition sequence, strand 1 | dna | 21 | — | — |
| F | E1 recognition sequence, strand 2 | dna | 21 | — | — |
| A, C | Replication protein E1 | protein | 145 | 43% helix, 26% strand | P03116 |
| B | Replication protein E1 | protein | 148 | 45% helix, 22% strand | P03116 |
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 547 | 0.61 | 0.75 | 36 | empty |
| 2 | 70 | 0.41 | 0.80 | 15 | empty |
| 3 | 70 | 0.40 | 0.80 | 16 | empty |
| 4 | 103 | 0.34 | 0.73 | 18 | empty |
| 5 | 101 | 0.34 | 0.74 | 17 | empty |
Interfaces
9 interfaces between chains.
- D–F · 907 Ų buried · 67 hydrogen bonds · nucleic-nucleic
- A–C · 461 Ų buried · 2 hydrogen bonds · protein-protein
- F–A · 284 Ų buried · 7 hydrogen bonds · protein-nucleic
- D–C · 276 Ų buried · 6 hydrogen bonds · protein-nucleic
- D–A · 224 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 1KSY · Crystal Structures of Two Intermediates in the Assembly of the Papillomavirus Replication… · the same entry in another collection · chain D against D, 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 P03116
- Elsewhere: RCSB PDB 1KSY · PDBe 1KSY · UniProt P03116
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