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X-ray structure of the tetrameric mutant of the B1 domain of streptococcal protein G

Analyse X-ray structure of the tetrameric mutant of the B1 domain of streptococcal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1MVK
Type: protein
Length: 557 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Immunoglobulin G binding protein G
UniProt: P06654
Ligands: SO4
Pockets: 5 · best druggability 0.70

Structure

x-ray diffraction · 7 distinct chains · 29% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, F, J, K	Immunoglobulin G binding protein G	protein	46	28% helix, 35% strand	P06654
D	Immunoglobulin G binding protein G	protein	45	31% helix, 36% strand	P06654
E	Immunoglobulin G binding protein G	protein	45	31% helix, 36% strand	P06654
G	Immunoglobulin G binding protein G	protein	47	28% helix, 34% strand	P06654
H	Immunoglobulin G binding protein G	protein	50	28% helix, 32% strand	P06654
I	Immunoglobulin G binding protein G	protein	48	29% helix, 31% strand	P06654
L	Immunoglobulin G binding protein G	protein	46	30% helix, 35% strand	P06654

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains A, B, C, D, E, F, G, H, I, J, K, L

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	745	0.70	0.77	104	SO4
2	233	0.53	0.77	33	empty
3	168	0.51	0.79	26	SO4
4	111	0.38	0.75	28	SO4
5	50	0.37	0.80	14	empty

Interfaces

29 interfaces between chains.

K–L · 1271 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 1266 Å² buried · 12 hydrogen bonds · protein-protein
G–H · 1239 Å² buried · 10 hydrogen bonds · protein-protein
E–F · 1236 Å² buried · 13 hydrogen bonds · protein-protein
I–J · 1207 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

1MVK · X-ray structure of the tetrameric mutant of the B1 domain of streptococcal protein G · 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 P06654
Elsewhere: RCSB PDB 1MVK · PDBe 1MVK · UniProt P06654

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