MolNFT v1 · #102071 · protein
Bldd ctd-C-di-gmp complex
4OAY · DNA-binding protein: “Bldd ctd-C-di-gmp complex”. X-ray diffraction, 1 ligand (C2E), 9 pockets (best druggability 0.74). MolNFT v1 #102071 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4OAY
- Type
- protein
- Length
- 928 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-binding protein
- UniProt
- F2RCL8
- Ligands
- C2E
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 62% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-binding protein | protein | 80 | 63% helix, 8% strand | F2RCL8 |
| B | DNA-binding protein | protein | 73 | 60% helix, 11% strand | F2RCL8 |
| K, J, R, D, N | DNA-binding protein | protein | 79 | 61% helix, 8% strand | F2RCL8 |
| H, E, G, F, M | DNA-binding protein | protein | 76 | 63% 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 · 24 copies · chains A, N, M, B, K, R, J, D, H, G, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 792 | 0.74 | 0.79 | 59 | C2E |
| 2 | 215 | 0.52 | 0.77 | 31 | empty |
| 3 | 66 | 0.34 | 0.76 | 15 | empty |
| 4 | 85 | 0.32 | 0.73 | 15 | C2E |
| 5 | 63 | 0.30 | 0.74 | 12 | empty |
Interfaces
14 interfaces between chains.
- A–B · 467 Ų buried · 7 hydrogen bonds · protein-protein
- N–M · 440 Ų buried · 3 hydrogen bonds · protein-protein
- K–E · 365 Ų buried · 8 hydrogen bonds · protein-protein
- G–N · 316 Ų buried · 3 hydrogen bonds · protein-protein
- G–M · 121 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 4OAY · BldD CTD-c-di-GMP complex · the same entry in another collection · chain A against A, 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 4OAY · PDBe 4OAY · UniProt F2RCL8
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