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Dtd from plasmodium falciparum in complex with D-lysine

Analyse Dtd from plasmodium falciparum in complex with D-lysine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3KO7
Type: protein
Length: 912 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
Ligands: DLY
Pockets: 12 · best druggability 0.75

Structure

x-ray diffraction · 6 distinct chains · 23% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-)	protein	161	22% helix, 41% strand	Q8IIS0
B	D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-)	protein	159	24% helix, 42% strand	Q8IIS0
C	D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-)	protein	151	25% helix, 42% strand	Q8IIS0
D	D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-)	protein	150	23% helix, 43% strand	Q8IIS0
E	D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-)	protein	149	23% helix, 43% strand	Q8IIS0
F	D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-)	protein	142	24% helix, 44% strand	Q8IIS0

Ligands and binding sites

DLY · D-lysine · ligand · chains C, D

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

Pockets

12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	919	0.75	0.78	64	empty
2	163	0.56	0.81	32	empty
3	137	0.52	0.80	28	empty
4	174	0.51	0.78	30	empty
5	129	0.50	0.79	28	DLY

Interfaces

6 interfaces between chains.

A–B · 1958 Å² buried · 45 hydrogen bonds · protein-protein
C–D · 1873 Å² buried · 49 hydrogen bonds · protein-protein
E–F · 1673 Å² buried · 46 hydrogen bonds · protein-protein
C–E · 298 Å² buried · 1 hydrogen bond · protein-protein
D–E · 74 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3KO7 · DTD from Plasmodium falciparum in complex with D-Lysine · the same entry in another collection · chain E against E, TM-score 1.00
Q8IIS0 · AlphaFold monomer V2.0 prediction for D-aminoacyl-tRNA deacylase (Q8IIS0) · 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 Q8IIS0
Elsewhere: RCSB PDB 3KO7 · PDBe 3KO7 · UniProt Q8IIS0

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