MolNFT v1 · #124511 · protein
Structure of 1.75 a bldd C-domain-C-di-gmp complex
5KHD · DNA-binding protein: “Structure of 1.75 a bldd C-domain-C-di-gmp complex”. X-ray diffraction, 1 ligand (C2E). MolNFT v1 #124511 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5KHD
- Type
- protein
- Length
- 145 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-binding protein
- UniProt
- F2RCL8
- Ligands
- C2E
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | DNA-binding protein | protein | 73 | 58% helix, 12% strand | F2RCL8 |
| A | DNA-binding protein | protein | 72 | 61% helix, 13% strand | F2RCL8 |
Ligands and binding sites
- C2E · 9,9'-[(2r,3r,3as,5s,7ar,9r,10r,10as,12s,14ar)-3,5,10, 12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3, 2-D:3',2'-J][1,3,7,9,2, 8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) · ligand · 4 copies · chains R, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
1 interface between chains.
- R–A · 82 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5KHD · Structure of 1.75 A BldD C-domain-c-di-GMP complex · the same entry in another collection · chain R against R, 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 F2RCL8
- Elsewhere: RCSB PDB 5KHD · PDBe 5KHD · UniProt F2RCL8
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