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Cryo-EM structure of the drosophila CTP synthase substrate-bound filament

Analyse Cryo-EM structure of the drosophila CTP synthase substrate-bound filament in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6L6Z
Type: protein
Length: 4,496 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CTP synthase
EC: 6.3.4.2
UniProt: Q9VUL1
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 1 distinct chain · 31% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, A, B, C, H, E, F, G	CTP synthase (EC 6.3.4.2)	protein	562	31% helix, 15% strand	Q9VUL1

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	670	0.86	0.91	96	empty
2	352	0.84	0.93	77	empty
3	429	0.83	0.90	66	empty
4	1064	0.82	0.83	93	empty
5	261	0.82	0.93	37	empty

Interfaces

16 interfaces between chains.

A–B · 1375 Å² buried · 9 hydrogen bonds · protein-protein
E–F · 1373 Å² buried · 8 hydrogen bonds · protein-protein
D–C · 1354 Å² buried · 9 hydrogen bonds · protein-protein
H–G · 1353 Å² buried · 9 hydrogen bonds · protein-protein
H–E · 1134 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

6L6Z · Cryo-EM structure of the Drosophila CTP synthase substrate-bound filament · the same entry in another collection · chain G against G, TM-score 1.00
Q9VUL1 · AlphaFold monomer V2.0 prediction for CTP synthase (Q9VUL1) · a predicted model of the same protein · chain D against A, TM-score 0.95

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 Q9VUL1
Elsewhere: RCSB PDB 6L6Z · PDBe 6L6Z · UniProt Q9VUL1

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