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Structure of DHFR with bound dap, P-abg and NADP

Analyse Structure of DHFR with bound dap, P-abg and NADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5UIO
Type: protein
Length: 800 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dihydrofolate reductase
EC: 1.5.1.3
UniProt: P0ABQ4
Ligands: LG3, 8DM, NAP
Pockets: 9 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 24% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Dihydrofolate reductase (EC 1.5.1.3)	protein	160	24% helix, 33% strand	P0ABQ4

Ligands and binding sites

LG3 · Pyrimidine-2,4-diamine · ligand · 5 copies · chains A, B, C, D, E
8DM · N-(4-aminobenzene-1-carbonyl)-L-glutamic acid · ligand · 4 copies · chains A, C, D, E
NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, C, D, E
BME · Beta-mercaptoethanol · additive · 4 copies · chains B, C, D, E
FMT · Formic acid · additive · 2 copies · chains B, C

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

Pockets

9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	589	0.78	0.84	50	LG3, FMT
2	571	0.75	0.82	52	LG3, 8DM
3	747	0.73	0.79	78	LG3, 8DM, NAP
4	459	0.71	0.82	60	LG3, 8DM, NAP
5	441	0.67	0.79	43	LG3, 8DM, NAP

Interfaces

7 interfaces between chains.

B–C · 613 Å² buried · 11 hydrogen bonds · protein-protein
D–E · 512 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 440 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 308 Å² buried · 2 hydrogen bonds · protein-protein
B–E · 283 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (additive adduct).

Compared structures

5UIO · structure of DHFR with bound DAP, p-ABG and NADP · the same entry in another collection · chain E against E, TM-score 1.00
P0ABQ4 · AlphaFold monomer V2.0 prediction for dihydrofolate reductase (P0ABQ4) · a predicted model of the same protein · chain D against A, TM-score 0.99

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 P0ABQ4
Elsewhere: RCSB PDB 5UIO · PDBe 5UIO · UniProt P0ABQ4

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