MolNFT v1 · #160262 · protein

Crystal structure of ts-DHFR from cryptosporidium hominis in complex with NADPH, fdump and 3-(2-(4-((2-amino-4-oxo-4,7-dihydro-3H- PYRROLO[2,3-D]PYRIMIDIN-5-YL)METHYL)BENZAMIDO)PHENYL)PROPANOIC acid.

6PFB · Bifunctional dihydrofolate reductase-thymidylate synthase: “Crystal structure of ts-DHFR from cryptosporidium hominis in complex with NADPH, fdump and…”. X-ray diffraction, 4 ligands (NDP, UFP, OG4), 20 pockets (best druggability…

PDB: 6PFB
Type: protein
Length: 2,527 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bifunctional dihydrofolate reductase-thymidylate synthase
UniProt: A0A0S4TER9
Ligands: NDP, UFP, OG4, MTX
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 26% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, E	Bifunctional dihydrofolate reductase-thymidylate synthase	protein	505	26% helix, 24% strand	A0A0S4TER9
C, D	Bifunctional dihydrofolate reductase-thymidylate synthase	protein	506	26% helix, 25% strand	A0A0S4TER9

Ligands and binding sites

NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 5 copies · chains A, B, C, D, E
UFP · 5-fluoro-2'-deoxyuridine-5'-monophosphate · ligand · 5 copies · chains A, B, C, D, E
OG4 · 3-[2-({4-[(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzene-1-carbonyl}amino) phenyl]propanoic acid · ligand · 5 copies · chains A, B, C, D, E
MTX · Methotrexate · ligand · 5 copies · chains A, 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, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	350	0.78	0.88	38	UFP, OG4
2	416	0.78	0.87	45	UFP, OG4
3	822	0.78	0.81	70	NDP, MTX
4	829	0.78	0.81	72	NDP, MTX
5	806	0.77	0.81	72	NDP, MTX

Interfaces

7 interfaces between chains.

C–D · 4398 Å² buried · 62 hydrogen bonds · protein-protein
A–B · 4380 Å² buried · 64 hydrogen bonds · protein-protein
C–E · 226 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 226 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 214 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

6PFB · Crystal structure of TS-DHFR from Cryptosporidium hominis in complex with NADPH, FdUMP… · 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 A0A0S4TER9
Elsewhere: RCSB PDB 6PFB · PDBe 6PFB · UniProt A0A0S4TER9

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