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Crystal structure AMA1 from toxoplasma gondii

Analyse Crystal structure AMA1 from toxoplasma gondii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2X2Z
Type: protein
Length: 1,571 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Apical membrane antigen 1, putative
UniProt: B6KAM0
Ligands: NAG
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 4 distinct chains · 15% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Apical membrane antigen 1, putative	protein	407	15% helix, 28% strand	B6KAM0
B	Apical membrane antigen 1, putative	protein	401	16% helix, 27% strand	B6KAM0
D	Apical membrane antigen 1, putative	protein	367	14% helix, 29% strand	B6KAM0
E	Apical membrane antigen 1, putative	protein	396	15% helix, 30% strand	B6KAM0

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, D, E
GOL · Glycerol · additive · chains D

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

Pockets

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	860	0.82	0.85	104	empty
2	334	0.63	0.79	30	empty
3	158	0.58	0.82	33	empty
4	142	0.56	0.81	36	empty
5	126	0.54	0.82	29	empty

Interfaces

5 interfaces between chains.

A–B · 810 Å² buried · 6 hydrogen bonds · protein-protein
D–E · 484 Å² buried · 2 hydrogen bonds · protein-protein
B–E · 472 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 406 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 160 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 30 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

2X2Z · Crystal structure AMA1 from Toxoplasma gondii · the same entry in another collection · chain E against E, TM-score 1.00
B6KAM0 · AlphaFold monomer V2.0 prediction for apical membrane antigen 1 (B6KAM0) · 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 B6KAM0
Elsewhere: RCSB PDB 2X2Z · PDBe 2X2Z · UniProt B6KAM0

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