MolNFT v1 · #90736 · protein

Crystal structure of ydiv and flhd complex

4ES4 · Putative cyclic di-gmp regulator cdgr: “Crystal structure of ydiv and flhd complex”. X-ray diffraction, 15 pockets (best druggability 0.79). MolNFT v1 #90736 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

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.

Pocket	Volume (Å³)	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 Å² buried · 32 hydrogen bonds · protein-protein
B–H · 2314 Å² buried · 33 hydrogen bonds · protein-protein
E–F · 1022 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 1022 Å² buried · 11 hydrogen bonds · protein-protein
G–H · 1022 Å² 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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