MolNFT v1 · #134280 · protein

Crystal structure of aquifex aeolicus hfq at 1.5A

5SZD · RNA-binding protein hfq: “Crystal structure of aquifex aeolicus hfq at 1.5A”. X-ray diffraction, 2 ligands (GAI, CL), 14 pockets (best druggability 0.77). MolNFT v1 #134280 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5SZD
Type: protein
Length: 848 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA-binding protein hfq
UniProt: O66512
Ligands: GAI, CL
Pockets: 14 · best druggability 0.77

Structure

x-ray diffraction · 5 distinct chains · 22% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F	RNA-binding protein hfq	protein	72	22% helix, 46% strand	O66512
B	RNA-binding protein hfq	protein	70	23% helix, 47% strand	O66512
C, H, I, J, K, L	RNA-binding protein hfq	protein	71	21% helix, 46% strand	O66512
D, E	RNA-binding protein hfq	protein	69	23% helix, 48% strand	O66512
G	RNA-binding protein hfq	protein	70	21% helix, 44% strand	O66512

Ligands and binding sites

GAI · Guanidine · ligand · 8 copies · chains A, F, I, J, B, K, C, L, D, E, G, H
CL · Chloride ion · ion · 7 copies · chains F, D, G, E, H, I, A, J, B, K, C, L
MRD · (4R)-2-methylpentane-2,4-diol · additive · 13 copies · chains A, B, F, C, D, E, G, H, I, J, K, L
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 12 copies · chains A, B, C, D, E, G, H, I, J, K, L
PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains G, L, I, J, K

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

Pockets

14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	838	0.77	0.80	58	MRD
2	597	0.76	0.82	56	GAI, MPD, CL
3	203	0.74	0.90	43	GAI, MPD, CL
4	213	0.74	0.89	45	GAI, MPD, CL
5	249	0.73	0.87	37	GAI, MPD, CL

Interfaces

24 interfaces between chains.

B–C · 1026 Å² buried · 17 hydrogen bonds · protein-protein
J–K · 984 Å² buried · 18 hydrogen bonds · protein-protein
K–L · 957 Å² buried · 19 hydrogen bonds · protein-protein
H–I · 949 Å² buried · 20 hydrogen bonds · protein-protein
G–H · 948 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

O66512 · AlphaFold monomer V2.0 prediction for RNA-binding protein hfq (O66512) · a predicted model of the same protein · chain D against A, TM-score 0.96

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 O66512
Elsewhere: RCSB PDB 5SZD · PDBe 5SZD · UniProt O66512

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