MolNFT v1 · #117088 · protein

Crystal structure of rethreaded DHFR

5DXV: “Crystal structure of rethreaded DHFR”. X-ray diffraction, 2 ligands (NAP, CL), 3 pockets (best druggability 0.44). MolNFT v1 #117088 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5DXV
Type: protein
Length: 294 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rethreaded DHFR
Ligands: NAP, CL
Pockets: 3 · best druggability 0.44

Structure

x-ray diffraction · 2 distinct chains · 26% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Rethreaded DHFR	protein	149	26% helix, 34% strand	—
B	Rethreaded DHFR	protein	145	26% helix, 33% strand	—

Ligands and binding sites

NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
CL · Chloride ion · ion · 2 copies · chains A, B
PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · 2 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	179	0.44	0.74	23	PEG
2	192	0.44	0.73	24	PEG
3	50	0.27	0.74	13	CL

Interfaces

1 interface between chains.

A–B · 220 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (artifact).

Compared structures

5DXV · Crystal structure of Rethreaded DHFR · 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
Elsewhere: RCSB PDB 5DXV · PDBe 5DXV

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