MolNFT v1 · #176508 · protein

Crystal structure of wild type brugia malayi thymidylate synthase complexed with 2'-deoxyuridine monophosphate and methotrexate

7DP4: “Crystal structure of wild type brugia malayi thymidylate synthase complexed with 2'-deoxyuridine…”. X-ray diffraction, 2 ligands (UMP, MTX), 1 pocket (best druggability 0.67). MolNFT v1 #176508 on GenesisL1: 3D structure, binding…

PDB: 7DP4
Type: protein
Length: 287 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thymidylate synthase
EC: 2.1.1.45
UniProt: A0A4E9EZW9
Ligands: UMP, MTX
Pockets: 1 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thymidylate synthase (EC 2.1.1.45)	protein	287	36% helix, 24% strand	A0A4E9EZW9

Ligands and binding sites

UMP · 2'-deoxyuridine 5'-monophosphate · ligand · chains A
MTX · Methotrexate · ligand · chains A
BME · Beta-mercaptoethanol · additive · 5 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	484	0.67	0.78	43	UMP, MTX

Modifications

Observed in the structure: 3 covalent (additive adduct).

Compared structures

7DP4 · Crystal structure of wild type Brugia malayi thymidylate synthase complexed with… · the same entry in another collection · chain A 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 A0A4E9EZW9
Elsewhere: RCSB PDB 7DP4 · PDBe 7DP4 · UniProt A0A4E9EZW9

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