Research workbench

Structural insights into the molecular organization of the S-layer from clostridium difficile

Analyse Structural insights into the molecular organization of the S-layer from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3CVZ
Type: protein
Length: 976 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: S-layer protein
UniProt: Q1JU94
Ligands: GLY, PO4
Pockets: 6 · best druggability 0.64

Structure

x-ray diffraction · 3 distinct chains · 22% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	S-layer protein	protein	248	22% helix, 33% strand	Q1JU94
B, D	S-layer protein	protein	242	21% helix, 32% strand	Q1JU94
C	S-layer protein	protein	244	23% helix, 34% strand	Q1JU94

Ligands and binding sites

GLY · Glycine · ligand · 3 copies · chains A, B, C, D
PO4 · Phosphate ion · ion · chains A

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	447	0.64	0.78	64	empty
2	427	0.61	0.76	51	empty
3	237	0.57	0.78	30	empty
4	187	0.53	0.78	24	empty
5	144	0.46	0.77	19	empty

Interfaces

3 interfaces between chains.

A–D · 537 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 501 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 434 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

3CVZ · Structural insights into the molecular organization of the S-layer from Clostridium… · 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 Q1JU94
Elsewhere: RCSB PDB 3CVZ · PDBe 3CVZ · UniProt Q1JU94

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.