MolNFT v1 · #164439 · protein + DNA
Structure of the plasmodium falciparum SIP2 DNA-binding AP2 tandem repeat in complex with two SPE2 half-sites
6SY0 · Transcription factor with AP2 DOMAIN(S): “Structure of the plasmodium falciparum SIP2 DNA-binding AP2 tandem repeat in complex with two SPE2 half-sites”. X-ray diffraction, 10 pockets (best druggability 0.63). MolNFT v1 #164439 on…
- PDB
- 6SY0
- Type
- protein + DNA
- Length
- 481 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription factor with AP2 DOMAIN(S); DNA (5'…
- UniProt
- C6KSN9
- Pockets
- 10 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcription factor with AP2 DOMAIN(S) | protein | 137 | 35% helix, 37% strand | C6KSN9 |
| B | Transcription factor with AP2 DOMAIN(S) | protein | 132 | 32% helix, 39% strand | C6KSN9 |
| C | Transcription factor with AP2 DOMAIN(S) | protein | 104 | 34% helix, 29% strand | C6KSN9 |
| E, F, G, H, K, L | DNA (5'- D(*GP*GP*TP*GP*CP*AP*CP*CP*TP*AP*GP*GP*TP*GP*CP*AP*CP*C)-3') | dna | 18 | — | — |
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 484 | 0.63 | 0.76 | 36 | empty |
| 2 | 482 | 0.62 | 0.76 | 51 | empty |
| 3 | 532 | 0.62 | 0.75 | 43 | empty |
| 4 | 221 | 0.50 | 0.76 | 24 | empty |
| 5 | 119 | 0.47 | 0.79 | 18 | empty |
Interfaces
16 interfaces between chains.
- E–H · 830 Ų buried · 72 hydrogen bonds · nucleic-nucleic
- K–L · 826 Ų buried · 74 hydrogen bonds · nucleic-nucleic
- F–G · 824 Ų buried · 67 hydrogen bonds · nucleic-nucleic
- B–E · 634 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–K · 633 Ų buried · 19 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 3 modified (nonstandard).
Compared structures
- 6SY0 · Structure of the Plasmodium falciparum SIP2 DNA-binding AP2 tandem repeat in complex with… · 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 C6KSN9
- Elsewhere: RCSB PDB 6SY0 · PDBe 6SY0 · UniProt C6KSN9
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