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Alanine scanning mutagenesis identifies an asparagine-arginine-lysine triad essential to assembly of the shell of the pdu microcompartment

Analyse Alanine scanning mutagenesis identifies an asparagine-arginine-lysine triad… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4P2S
Type: protein
Length: 792 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative propanediol utilization protein pdua
UniProt: V1FW89
Ligands: SO4
Pockets: 4 · best druggability 0.48

Structure

x-ray diffraction · 6 distinct chains · 37% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, I	Putative propanediol utilization protein pdua	protein	88	35% helix, 39% strand	V1FW89
B	Putative propanediol utilization protein pdua	protein	89	38% helix, 37% strand	V1FW89
C, E, G	Putative propanediol utilization protein pdua	protein	87	41% helix, 38% strand	V1FW89
D	Putative propanediol utilization protein pdua	protein	88	35% helix, 39% strand	V1FW89
F	Putative propanediol utilization protein pdua	protein	89	38% helix, 38% strand	V1FW89
H	Putative propanediol utilization protein pdua	protein	89	35% helix, 38% strand	V1FW89

Ligands and binding sites

SO4 · Sulfate ion · ion · 5 copies · chains A, H, D, C, I
GOL · Glycerol · additive · 7 copies · chains A, B, C, D, E, F, G, H, I
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains D

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

Pockets

4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	121	0.48	0.79	25	GOL
2	241	0.46	0.73	26	GOL, SO4
3	93	0.35	0.74	21	empty
4	64	0.35	0.77	18	SO4

Interfaces

10 interfaces between chains.

C–D · 907 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 895 Å² buried · 11 hydrogen bonds · protein-protein
D–E · 866 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 865 Å² buried · 14 hydrogen bonds · protein-protein
H–I · 862 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

4P2S · Alanine Scanning Mutagenesis Identifies an Asparagine-Arginine-Lysine Triad Essential to… · the same entry in another collection · chain A against A, 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 V1FW89
Elsewhere: RCSB PDB 4P2S · PDBe 4P2S · UniProt V1FW89

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