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Crystal structure of the variable region of plasmodium rifin #6 (PF3D7_1400600) in complex with LAIR1 (with T67L, N69S and A77T mutations)

Analyse Crystal structure of the variable region of plasmodium rifin #6 (PF3D7_1400600)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7F9L
Type: protein
Length: 1,548 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rifin; Leukocyte-associated immunoglobulin-like receptor 1
UniProt: Q8IM82, Q6GTX8
Pockets: 17 · best druggability 0.75

Structure

x-ray diffraction · 7 distinct chains · 50% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Rifin	protein	162	72% helix, 2% strand	Q8IM82
C	Rifin	protein	158	72% helix, 3% strand	Q8IM82
E	Rifin	protein	160	71% helix, 3% strand	Q8IM82
F	Rifin	protein	154	75% helix, 3% strand	Q8IM82
G, H, I, J	Leukocyte-associated immunoglobulin-like receptor 1	protein	99	0% helix, 55% strand	Q6GTX8
K	Leukocyte-associated immunoglobulin-like receptor 1	protein	97	0% helix, 49% strand	Q6GTX8
L	Leukocyte-associated immunoglobulin-like receptor 1	protein	97	3% helix, 45% strand	Q6GTX8

Pockets

17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	683	0.75	0.81	74	empty
2	613	0.71	0.79	53	empty
3	566	0.65	0.76	63	empty
4	400	0.60	0.76	36	empty
5	322	0.56	0.75	37	empty

Interfaces

21 interfaces between chains.

D–F · 1273 Å² buried · 5 hydrogen bonds · protein-protein
B–E · 1264 Å² buried · 5 hydrogen bonds · protein-protein
B–G · 919 Å² buried · 15 hydrogen bonds · protein-protein
A–F · 735 Å² buried · 13 hydrogen bonds · protein-protein
F–L · 656 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

7F9L · Crystal structure of the variable region of Plasmodium RIFIN #6 (PF3D7_1400600) in… · the same entry in another collection · chain L against L, 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
Every structure of UniProt Q8IM82
Every structure of UniProt Q6GTX8
Elsewhere: RCSB PDB 7F9L · PDBe 7F9L · UniProt Q8IM82 · UniProt Q6GTX8

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