MolNFT v1 · #147446 · protein + DNA
Crystal structure of SRY.HCGAS-21BP dsdna complex
6EDB · Sex-determining region Y PROTEIN,CYCLIC gmp-AMP synthase: “Crystal structure of SRY.HCGAS-21BP dsdna complex”. X-ray diffraction, 1 ligand (ZN), 6 pockets (best druggability 0.77). MolNFT v1 #147446 on GenesisL1: 3D structure…
- PDB
- 6EDB
- Type
- protein + DNA
- Length
- 466 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sex-determining region Y PROTEIN,CYCLIC gmp-AMP synthase; DNA (5'…
- EC
- 2.7.7.86
- UniProt
- Q05066, Q8N884
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sex-determining region Y PROTEIN,CYCLIC gmp-AMP synthase (EC 2.7.7.86) | protein | 357 | 39% helix, 17% strand | Q05066, Q8N884 |
| B | Sex-determining region Y PROTEIN,CYCLIC gmp-AMP synthase (EC 2.7.7.86) | protein | 67 | 63% helix, 0% strand | Q05066, Q8N884 |
| C | DNA (5'- D(*CP*GP*AP*TP*CP*CP*GP*GP*GP*AP*TP*CP*TP*AP*AP*AP*CP*AP*AP*TP*G)- 3') | dna | 21 | — | — |
| D | DNA (5'- D(*GP*CP*AP*TP*TP*GP*TP*TP*TP*AP*GP*AP*TP*CP*CP*CP*GP*GP*AP*TP*C)- 3') | dna | 21 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1135 | 0.77 | 0.79 | 82 | empty |
| 2 | 895 | 0.74 | 0.78 | 59 | empty |
| 3 | 119 | 0.50 | 0.81 | 21 | empty |
| 4 | 58 | 0.33 | 0.77 | 12 | empty |
| 5 | 58 | 0.33 | 0.77 | 17 | empty |
Interfaces
5 interfaces between chains.
- C–D · 915 Ų buried · 62 hydrogen bonds · nucleic-nucleic
- B–D · 592 Ų buried · 3 hydrogen bonds · protein-nucleic
- B–C · 428 Ų buried · 3 hydrogen bonds · protein-nucleic
- A–C · 371 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–D · 329 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 6EDB · Crystal structure of SRY.hcGAS-21bp dsDNA complex · the same entry in another collection · chain D against D, TM-score 1.00
- Q8N884 · AlphaFold monomer V2.0 prediction for cyclic gmp-AMP synthase (Q8N884) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q05066 · AlphaFold monomer V2.0 prediction for sex-determining region Y protein (Q05066) · a predicted model of the same protein · chain B against A, TM-score 0.92
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 Q05066
- Every structure of UniProt Q8N884
- Elsewhere: RCSB PDB 6EDB · PDBe 6EDB · UniProt Q05066 · UniProt Q8N884
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