MolNFT v1 · #59217 · protein + DNA
Csl (lag-1) bound to DNA with lin-12 ram peptide, P212121
3BRD · DNA (5'- D(*DTP*DTP*DAP*DCP*DTP*DGP*DTP*DGP*DGP*DGP*DAP*DAP*…: “Csl (lag-1) bound to DNA with lin-12 ram peptide, P212121”. X-ray diffraction, 7 pockets (best druggability 0.76). MolNFT v1 #59217 on GenesisL1: 3D structure, binding…
- PDB
- 3BRD
- Type
- protein + DNA
- Length
- 472 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*DTP*DTP*DAP*DCP*DTP*DGP*DTP*DGP*DGP*DGP*DAP*DAP*DAP*DGP*DA)-3'); DNA (5'…
- UniProt
- Q9TYY1, P14585
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA (5'- D(*DTP*DTP*DAP*DCP*DTP*DGP*DTP*DGP*DGP*DGP*DAP*DAP*DAP*DGP*DA)-3') | dna | 15 | — | — |
| C | DNA (5'- D(*DAP*DAP*DTP*DCP*DTP*DTP*DTP*DCP*DCP*DCP*DAP*DCP*DAP*DGP*DT)-3') | dna | 15 | — | — |
| A | Lin-12 and glp-1 phenotype protein 1, isoform a | protein | 427 | 11% helix, 46% strand | Q9TYY1 |
| D | Protein lin-12 | protein | 15 | 0% helix, 40% strand | P14585 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 10 copies · chains C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 613 | 0.76 | 0.82 | 52 | empty |
| 2 | 182 | 0.52 | 0.78 | 32 | EDO |
| 3 | 131 | 0.43 | 0.76 | 23 | EDO |
| 4 | 74 | 0.38 | 0.77 | 15 | empty |
| 5 | 78 | 0.35 | 0.76 | 17 | EDO |
Interfaces
4 interfaces between chains.
- A–D · 993 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 602 Ų buried · 58 hydrogen bonds · nucleic-nucleic
- C–A · 596 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–A · 528 Ų buried · 15 hydrogen bonds · protein-nucleic
Compared structures
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 Q9TYY1
- Every structure of UniProt P14585
- Elsewhere: RCSB PDB 3BRD · PDBe 3BRD · UniProt Q9TYY1 · UniProt P14585
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