MolNFT v1 · #165568 · protein

The structure of the streptococcus gordonii surface protein sspb in complex with tev peptide provides clues to the adherence of oral streptococcal adherence to salivary agglutinin

6TZL · Surface protein adhesin: “The structure of the streptococcus gordonii surface protein sspb in complex with tev peptide provides clues…”. X-ray diffraction, 1 ligand (SO4), 15 pockets (best druggability 0.75). MolNFT v1 #165568 on…

PDB: 6TZL
Type: protein
Length: 1,575 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Surface protein adhesin
UniProt: C9E3B4
Ligands: SO4
Pockets: 15 · best druggability 0.75

Structure

x-ray diffraction · 4 distinct chains · 21% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Surface protein adhesin	protein	388	20% helix, 32% strand	C9E3B4
B	Surface protein adhesin	protein	384	20% helix, 32% strand	C9E3B4
C	Surface protein adhesin	protein	404	23% helix, 31% strand	C9E3B4
D	Surface protein adhesin	protein	399	22% helix, 31% strand	C9E3B4

Ligands and binding sites

SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D

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

Pockets

15 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	402	0.75	0.85	59	empty
2	527	0.71	0.80	76	empty
3	489	0.65	0.77	52	empty
4	479	0.64	0.77	48	empty
5	456	0.63	0.77	47	empty

Interfaces

4 interfaces between chains.

B–C · 604 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 503 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 425 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 412 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6TZL · The structure of the Streptococcus gordonii surface protein SspB in complex with TEV… · 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 C9E3B4
Elsewhere: RCSB PDB 6TZL · PDBe 6TZL · UniProt C9E3B4

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