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Crystal structure of A3VP1 of AGI/II of streptococcus mutans

Analyse Crystal structure of A3VP1 of AGI/II of streptococcus mutans in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3IPK
Type: protein
Length: 978 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: AGI/II
UniProt: A8R5D9
Ligands: PMS, CA, SO4
Pockets: 6 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	AGI/II	protein	489	30% helix, 26% strand	A8R5D9

Ligands and binding sites

PMS · phenylmethanesulfonic acid · ligand · 2 copies · chains A, B
CA · Calcium ion · metal · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	548	0.69	0.79	57	PMS, CA
2	444	0.64	0.78	43	PMS
3	217	0.57	0.79	33	empty
4	232	0.53	0.77	33	empty
5	89	0.33	0.74	18	empty

Interfaces

1 interface between chains.

A–B · 664 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

3IPK · Crystal Structure of A3VP1 of AgI/II of Streptococcus mutans · 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 A8R5D9
Elsewhere: RCSB PDB 3IPK · PDBe 3IPK · UniProt A8R5D9

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