MolNFT v1 · #117102 · protein

Y68T hfq from methanococcus jannaschii in complex with AMP

5DY9 · Hfq-like protein: “Y68T hfq from methanococcus jannaschii in complex with AMP”. X-ray diffraction, 4 ligands (AMP, NA, CL), 4 pockets (best druggability 0.77). MolNFT v1 #117102 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 5DY9
Type: protein
Length: 688 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hfq-like protein
UniProt: Q58830
Ligands: AMP, NA, CL, SO4
Pockets: 4 · best druggability 0.77

Structure

x-ray diffraction · 5 distinct chains · 13% helix, 55% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, G	Hfq-like protein	protein	56	14% helix, 57% strand	Q58830
B, F	Hfq-like protein	protein	58	12% helix, 55% strand	Q58830
C, H, J, K, L	Hfq-like protein	protein	57	14% helix, 56% strand	Q58830
E	Hfq-like protein	protein	60	13% helix, 53% strand	Q58830
I	Hfq-like protein	protein	59	12% helix, 54% strand	Q58830

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · 3 copies · chains A, F, D, E, G, L
NA · Sodium ion · metal · 2 copies · chains E, F, I, K
CL · Chloride ion · ion · 5 copies · chains E, I, H, F, K, J
SO4 · Sulfate ion · ion · 4 copies · chains C, D, E, I, F, J
GOL · Glycerol · additive · 3 copies · chains B, C, D
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · chains D, E, I, J, G, L
PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains G, H, E, I, F, J

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 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	1017	0.77	0.79	71	AMP, GOL, SO4
2	1082	0.77	0.79	68	AMP, CL, NA
3	530	0.69	0.79	44	SO4, PEG
4	248	0.53	0.76	23	CL, PEG

Interfaces

17 interfaces between chains.

E–F · 831 Å² buried · 13 hydrogen bonds · protein-protein
H–I · 819 Å² buried · 15 hydrogen bonds · protein-protein
A–F · 791 Å² buried · 15 hydrogen bonds · protein-protein
I–J · 788 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 785 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

5DY9 · Y68T Hfq from Methanococcus jannaschii in complex with AMP · the same entry in another collection · chain L against L, 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 Q58830
Elsewhere: RCSB PDB 5DY9 · PDBe 5DY9 · UniProt Q58830

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