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Crystal structure of dtd from plasmodium falciparum

Analyse Crystal structure of dtd from plasmodium falciparum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3KNP
Type: protein
Length: 927 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: D-tyrosyl-TRNA(TYR) deacylase
EC: 3.1.-.-
UniProt: Q8IIS0
Pockets: 11 · best druggability 0.68

Structure

x-ray diffraction · 5 distinct chains · 23% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-)	protein	159	24% helix, 39% strand	Q8IIS0
B	D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-)	protein	160	21% helix, 41% strand	Q8IIS0
D	D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-)	protein	152	23% helix, 37% strand	Q8IIS0
E	D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-)	protein	148	24% helix, 41% strand	Q8IIS0
F	D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-)	protein	149	25% helix, 44% strand	Q8IIS0

Pockets

11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	759	0.68	0.76	46	empty
2	454	0.63	0.76	58	empty
3	291	0.58	0.77	44	empty
4	188	0.56	0.80	32	empty
5	182	0.54	0.79	27	empty

Interfaces

8 interfaces between chains.

C–D · 1927 Å² buried · 45 hydrogen bonds · protein-protein
A–B · 1905 Å² buried · 36 hydrogen bonds · protein-protein
E–F · 1872 Å² buried · 44 hydrogen bonds · protein-protein
B–E · 723 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 169 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

3KNP · Crystal structure of DTD from Plasmodium falciparum · the same entry in another collection · chain F against F, TM-score 1.00
Q8IIS0 · AlphaFold monomer V2.0 prediction for D-aminoacyl-tRNA deacylase (Q8IIS0) · a predicted model of the same protein · chain F 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 Q8IIS0
Elsewhere: RCSB PDB 3KNP · PDBe 3KNP · UniProt Q8IIS0

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