MolNFT v1 · #26646 · protein + DNA
Crystal structure of multimeric DNA-binding protein SAC7D- GCN4 with DNA decamer
1WVL · 5'-D(*CP*CP*TP*AP*TP*AP*TP*AP*GP*G)-3': “Crystal structure of multimeric DNA-binding protein SAC7D- GCN4 with DNA decamer”. X-ray diffraction, 2 pockets (best druggability 0.60). MolNFT v1 #26646 on GenesisL1: 3D structure, binding…
- PDB
- 1WVL
- Type
- protein + DNA
- Length
- 179 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*CP*TP*AP*TP*AP*TP*AP*GP*G)-3'; DNA-binding proteins 7A/7B/7D, GCN4
- UniProt
- P13123
- Pockets
- 2 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'-D(*CP*CP*TP*AP*TP*AP*TP*AP*GP*G)-3' | dna | 9 | — | — |
| D | 5'-D(*CP*CP*TP*AP*TP*AP*TP*AP*GP*G)-3' | dna | 10 | — | — |
| A, B | DNA-binding proteins 7A/7B/7D, GCN4 | protein | 80 | 40% helix, 44% strand | P13123 |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.60 | 0.84 | 25 | empty |
| 2 | 123 | 0.41 | 0.76 | 23 | empty |
Interfaces
5 interfaces between chains.
- A–B · 703 Ų buried · 8 hydrogen bonds · protein-protein
- D–A · 425 Ų buried · 5 hydrogen bonds · protein-nucleic
- C–D · 411 Ų buried · 40 hydrogen bonds · nucleic-nucleic
- C–A · 363 Ų buried · 6 hydrogen bonds · protein-nucleic
- C–B · 23 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 1WVL · Crystal Structure of Multimeric DNA-binding Protein Sac7d-GCN4 with DNA decamer · the same entry in another collection · chain C against C, TM-score 1.00
- P13123 · AlphaFold monomer V2.0 prediction for DNA-binding protein 7D (P13123) · a predicted model of the same protein · chain A against A, TM-score 0.80
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 P13123
- Elsewhere: RCSB PDB 1WVL · PDBe 1WVL · UniProt P13123
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