MolNFT v1 · #179371 · protein

Crystal structure of DLC8 in complex with panoramix TQT+TQ peptide

7K3J · Dynein light chain 1, cytoplasmic: “Crystal structure of DLC8 in complex with panoramix TQT+TQ peptide”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.64). MolNFT v1 #179371 on GenesisL1: 3D structure, binding…

PDB: 7K3J
Type: protein
Length: 581 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dynein light chain 1, cytoplasmic; Protein panoramix
UniProt: Q24117, Q9W2H9
Ligands: SO4
Pockets: 3 · best druggability 0.64

Structure

x-ray diffraction · 5 distinct chains · 29% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G, I	Dynein light chain 1, cytoplasmic	protein	85	38% helix, 46% strand	Q24117
B	Protein panoramix	protein	25	12% helix, 56% strand	Q9W2H9
D, F	Protein panoramix	protein	11	0% helix, 64% strand	Q9W2H9
H	Protein panoramix	protein	25	0% helix, 60% strand	Q9W2H9
K	Dynein light chain 1, cytoplasmic	protein	84	38% helix, 45% strand	Q24117

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains A, C, G, I

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	511	0.64	0.76	55	empty
2	214	0.47	0.74	29	SO4
3	68	0.39	0.79	21	empty

Interfaces

17 interfaces between chains.

A–G · 934 Å² buried · 24 hydrogen bonds · protein-protein
I–K · 837 Å² buried · 25 hydrogen bonds · protein-protein
G–H · 811 Å² buried · 20 hydrogen bonds · protein-protein
B–I · 759 Å² buried · 19 hydrogen bonds · protein-protein
E–F · 579 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

7K3J · Crystal structure of dLC8 in complex with Panoramix TQT+TQ peptide · the same entry in another collection · chain K against K, TM-score 1.00
Q24117 · AlphaFold monomer V2.0 prediction for dynein light chain 1, cytoplasmic (Q24117) · a predicted model of the same protein · chain A 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 Q24117
Every structure of UniProt Q9W2H9
Elsewhere: RCSB PDB 7K3J · PDBe 7K3J · UniProt Q24117 · UniProt Q9W2H9

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