Research workbench
Crystal structure of ydiv and flhd complex
Analyse Crystal structure of ydiv and flhd complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ES4
- Type
- protein
- Length
- 1,132 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative cyclic di-gmp regulator cdgr; Flagellar transcriptional regulator flhd
- UniProt
- P76204, P0A8S9
- Pockets
- 15 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Putative cyclic di-gmp regulator cdgr | protein | 206 | 46% helix, 22% strand | P76204 |
| B, F | Flagellar transcriptional regulator flhd | protein | 80 | 65% helix, 4% strand | P0A8S9 |
| C, G | Putative cyclic di-gmp regulator cdgr | protein | 199 | 48% helix, 19% strand | P76204 |
| D, H | Flagellar transcriptional regulator flhd | protein | 81 | 62% helix, 4% strand | P0A8S9 |
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1116 | 0.79 | 0.81 | 88 | empty |
| 2 | 630 | 0.73 | 0.80 | 56 | empty |
| 3 | 286 | 0.57 | 0.77 | 33 | empty |
| 4 | 289 | 0.56 | 0.76 | 31 | empty |
| 5 | 70 | 0.49 | 0.83 | 18 | empty |
Interfaces
19 interfaces between chains.
- D–F · 2314 Ų buried · 32 hydrogen bonds · protein-protein
- B–H · 2314 Ų buried · 33 hydrogen bonds · protein-protein
- E–F · 1022 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1022 Ų buried · 11 hydrogen bonds · protein-protein
- G–H · 1022 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4ES4 · Crystal structure of YdiV and FlhD complex · the same entry in another collection · chain H against H, TM-score 1.00
- P76204 · AlphaFold monomer V2.0 prediction for putative anti-FLHC(2)FLHD(4) factor ydiv (P76204) · a predicted model of the same protein · chain C against A, TM-score 0.98
- P0A8S9 · AlphaFold monomer V2.0 prediction for flagellar transcriptional regulator flhd (P0A8S9) · a predicted model of the same protein · chain B against A, TM-score 0.87
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 P76204
- Every structure of UniProt P0A8S9
- Elsewhere: RCSB PDB 4ES4 · PDBe 4ES4 · UniProt P76204 · UniProt P0A8S9
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