MolNFT v1 · #109255 · protein

Crystal structure of binary complex GON7-PCC1

4WXA · EKC/KEOPS complex subunit PCC1: “Crystal structure of binary complex GON7-PCC1”. X-ray diffraction, 2 pockets (best druggability 0.58). MolNFT v1 #109255 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4WXA
Type: protein
Length: 432 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: EKC/KEOPS complex subunit PCC1; EKC/KEOPS complex subunit GON7
UniProt: Q3E833, P46984
Pockets: 2 · best druggability 0.58

Structure

x-ray diffraction · 5 distinct chains · 52% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	EKC/KEOPS complex subunit PCC1	protein	84	43% helix, 29% strand	Q3E833
C	EKC/KEOPS complex subunit PCC1	protein	78	41% helix, 31% strand	Q3E833
D	EKC/KEOPS complex subunit GON7	protein	68	62% helix, 15% strand	P46984
E	EKC/KEOPS complex subunit GON7	protein	69	62% helix, 16% strand	P46984
F	EKC/KEOPS complex subunit GON7	protein	49	57% helix, 22% strand	P46984

Ligands and binding sites

GOL · Glycerol · additive · chains A
ACT · Acetate ion · additive · chains A

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	352	0.58	0.76	41	empty
2	212	0.55	0.78	27	empty

Interfaces

6 interfaces between chains.

B–E · 1206 Å² buried · 18 hydrogen bonds · protein-protein
C–F · 1143 Å² buried · 19 hydrogen bonds · protein-protein
D–F · 369 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 363 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 350 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

P46984 · AlphaFold monomer V2.0 prediction for EKC/KEOPS complex subunit GON7 (P46984) · a predicted model of the same protein · chain F against A, TM-score 0.96
Q3E833 · AlphaFold monomer V2.0 prediction for EKC/KEOPS complex subunit PCC1 (Q3E833) · a predicted model of the same protein · chain C against A, TM-score 0.93

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 Q3E833
Every structure of UniProt P46984
Elsewhere: RCSB PDB 4WXA · PDBe 4WXA · UniProt Q3E833 · UniProt P46984

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.