MolNFT v1 · #12827 · protein + DNA
Crystal structures of two intermediates in the assembly of the papillomavirus replication initiation complex
1KSY · E1 recognition sequence, strand 1: “Crystal structures of two intermediates in the assembly of the papillomavirus replication initiation complex”. X-ray diffraction, 7 pockets (best druggability 0.61). MolNFT v1 #12827 on GenesisL1…
- 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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