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Structure of the tetramerization domain of nipah virus phosphoprotein

Analyse Structure of the tetramerization domain of nipah virus phosphoprotein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4GJW
Type: protein
Length: 781 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphoprotein
UniProt: Q9IK91
Ligands: ARG, CL
Pockets: 10 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 80% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, H	Phosphoprotein	protein	96	81% helix, 0% strand	Q9IK91
C, E, G	Phosphoprotein	protein	98	81% helix, 0% strand	Q9IK91
D	Phosphoprotein	protein	101	77% helix, 0% strand	Q9IK91
F	Phosphoprotein	protein	98	81% helix, 0% strand	Q9IK91

Ligands and binding sites

ARG · Arginine · ligand · chains B, D
CL · Chloride ion · ion · 6 copies · chains B, A, D, E, F, C, G, H
GOL · Glycerol · additive · 7 copies · chains C, F, A, D, B, G, E, H

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

Pockets

10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	93	0.77	0.98	24	empty
2	88	0.76	0.98	23	empty
3	113	0.43	0.77	18	empty
4	105	0.41	0.76	17	empty
5	100	0.40	0.76	17	empty

Interfaces

14 interfaces between chains.

E–F · 2462 Å² buried · 23 hydrogen bonds · protein-protein
C–G · 2460 Å² buried · 27 hydrogen bonds · protein-protein
A–D · 2448 Å² buried · 23 hydrogen bonds · protein-protein
B–H · 2434 Å² buried · 23 hydrogen bonds · protein-protein
B–D · 2427 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 modified (engineered).

Compared structures

4GJW · Structure of the tetramerization domain of Nipah virus phosphoprotein · the same entry in another collection · chain F against F, 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 Q9IK91
Elsewhere: RCSB PDB 4GJW · PDBe 4GJW · UniProt Q9IK91

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