Research workbench
Structure of the wt S. venezulae bldd-(ctd-C-di-GMP)2 assembly intermediate
Analyse Structure of the wt S. venezulae bldd-(ctd-C-di-GMP)2 assembly intermediate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TZD
- Type
- protein
- Length
- 296 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-binding protein
- UniProt
- F2RCL8
- Ligands
- C2E
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| J, B, C | DNA-binding protein | protein | 75 | 60% helix, 12% strand | F2RCL8 |
| A | DNA-binding protein | protein | 71 | 58% helix, 8% 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 J, B, C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 983 | 0.70 | 0.75 | 58 | C2E |
| 2 | 52 | 0.31 | 0.76 | 13 | empty |
Interfaces
5 interfaces between chains.
- B–A · 461 Ų buried · 4 hydrogen bonds · protein-protein
- J–C · 435 Ų buried · 3 hydrogen bonds · protein-protein
- C–A · 97 Ų buried · 0 hydrogen bonds · protein-protein
- J–B · 82 Ų buried · 1 hydrogen bond · protein-protein
- J–A · 63 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5TZD · Structure of the WT S. venezulae BldD-(CTD-c-di-GMP)2 assembly intermediate · the same entry in another collection · chain J against J, 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 5TZD · PDBe 5TZD · UniProt F2RCL8
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