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Crystal structure of ects W80G/DUMP/CB3717 complex

Analyse Crystal structure of ects W80G/DUMP/CB3717 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1KZJ
Type: protein
Length: 1,581 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thymidylate synthase
EC: 2.1.1.45
UniProt: P0A884
Ligands: UMP, CB3
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 2 distinct chains · 32% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, F	Thymidylate synthase (EC 2.1.1.45)	protein	264	33% helix, 26% strand	P0A884
E	Thymidylate synthase (EC 2.1.1.45)	protein	261	32% helix, 26% strand	P0A884

Ligands and binding sites

UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 6 copies · chains A, B, C, D, E, F
CB3 · 10-propargyl-5,8-dideazafolic acid · ligand · 6 copies · chains A, F, B, C, D, E

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

Pockets

20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	937	0.88	0.90	101	UMP, CB3
2	864	0.88	0.90	88	UMP, CB3
3	656	0.77	0.82	57	UMP, CB3
4	667	0.72	0.79	55	UMP, CB3
5	205	0.48	0.75	19	empty

Interfaces

5 interfaces between chains.

A–B · 2378 Å² buried · 35 hydrogen bonds · protein-protein
E–F · 2369 Å² buried · 34 hydrogen bonds · protein-protein
C–D · 2350 Å² buried · 36 hydrogen bonds · protein-protein
A–F · 630 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 564 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 modified, 4 covalent (carboxylation, covalent ligand).

Compared structures

1KZJ · Crystal Structure of EcTS W80G/dUMP/CB3717 Complex · the same entry in another collection · chain F against F, TM-score 1.00
P0A884 · AlphaFold monomer V2.0 prediction for thymidylate synthase (P0A884) · a predicted model of the same protein · chain C against A, TM-score 1.00

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 P0A884
Elsewhere: RCSB PDB 1KZJ · PDBe 1KZJ · UniProt P0A884

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