MolNFT v1 · #104965 · protein

Crystal structure of C1QL3 in P1 space group

4QQL · Complement C1Q-like protein 3: “Crystal structure of C1QL3 in P1 space group”. X-ray diffraction, 1 ligand (MG), 8 pockets (best druggability 0.72). MolNFT v1 #104965 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4QQL
Type: protein
Length: 1,172 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Complement C1Q-like protein 3
UniProt: Q9ESN4
Ligands: MG
Pockets: 8 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 0% helix, 55% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, E, F, G, H	Complement C1Q-like protein 3	protein	130	0% helix, 55% strand	Q9ESN4
C, I	Complement C1Q-like protein 3	protein	131	0% helix, 55% strand	Q9ESN4

Ligands and binding sites

MG · Magnesium ion · metal · 24 copies · chains A, B, C, D, F, E, H, I, G

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

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	55	0.72	0.99	15	MG
2	889	0.70	0.76	68	empty
3	284	0.54	0.75	37	empty
4	98	0.45	0.79	16	empty
5	122	0.44	0.77	22	MG

Interfaces

12 interfaces between chains.

B–C · 1065 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 1065 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 1063 Å² buried · 23 hydrogen bonds · protein-protein
D–F · 1061 Å² buried · 20 hydrogen bonds · protein-protein
E–H · 1059 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

4QQL · Crystal structure of C1QL3 in P1 space group · the same entry in another collection · chain H against H, TM-score 1.00
Q9ESN4 · AlphaFold monomer V2.0 prediction for complement C1Q-like protein 3 (Q9ESN4) · a predicted model of the same protein · chain B against A, TM-score 0.91

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 Q9ESN4
Elsewhere: RCSB PDB 4QQL · PDBe 4QQL · UniProt Q9ESN4

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