MolNFT v1 · #161657 · protein

Calpain small subunit 1, RNA-binding protein hfq

6QLB: “Calpain small subunit 1, RNA-binding protein hfq”. X-ray diffraction, 3 ligands (GUN, P4G, CA), 15 pockets (best druggability 0.73). MolNFT v1 #161657 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6QLB
Type: protein
Length: 943 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Calpain small subunit 1; RNA-binding protein hfq
UniProt: P04632, A0A376T1I0
Ligands: GUN, P4G, CA
Pockets: 15 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 55% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Calpain small subunit 1	protein	172	60% helix, 5% strand	P04632
B, C, D	Calpain small subunit 1	protein	173	61% helix, 6% strand	P04632
E, F, G, H	RNA-binding protein hfq	protein	63	22% helix, 48% strand	A0A376T1I0

Ligands and binding sites

GUN · Guanine · ligand · 4 copies · chains A, H, E, B, F, D, G
P4G · 1-ethoxy-2-(2-ethoxyethoxy)ethane · ligand · 2 copies · chains B, D, C
CA · Calcium ion · metal · 20 copies · chains A, B, C, D
EDO · 1,2-ethanediol · additive · chains A, B

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

Pockets

15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	73	0.73	0.98	19	empty
2	54	0.67	0.97	18	empty
3	676	0.65	0.75	72	CA
4	287	0.62	0.80	35	empty
5	268	0.57	0.78	35	EDO

Interfaces

15 interfaces between chains.

A–B · 2191 Å² buried · 27 hydrogen bonds · protein-protein
C–D · 2116 Å² buried · 24 hydrogen bonds · protein-protein
G–H · 750 Å² buried · 13 hydrogen bonds · protein-protein
E–F · 749 Å² buried · 9 hydrogen bonds · protein-protein
D–G · 546 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

6QLB · Calpain small subunit 1, RNA-binding protein Hfq · the same entry in another collection · chain H against H, TM-score 1.00
P04632 · AlphaFold monomer V2.0 prediction for calpain small subunit 1 (P04632) · a predicted model of the same protein · chain D against A, TM-score 0.99

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 P04632
Every structure of UniProt A0A376T1I0
Elsewhere: RCSB PDB 6QLB · PDBe 6QLB · UniProt P04632 · UniProt A0A376T1I0

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