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Catalytic domain of CD27L endolysin targeting clostridia difficile

Analyse Catalytic domain of CD27L endolysin targeting clostridia difficile in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3QAY
Type: protein
Length: 720 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Endolysin
UniProt: B6SBV8
Ligands: ZN, PO4
Pockets: 6 · best druggability 0.45

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Endolysin	protein	180	40% helix, 24% strand	B6SBV8

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
PO4 · Phosphate ion · ion · 14 copies · chains A, B, C, D

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

Pockets

6 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	229	0.45	0.73	24	empty
2	74	0.34	0.75	16	empty
3	72	0.32	0.75	15	empty
4	72	0.31	0.74	16	empty
5	74	0.30	0.73	19	PO4

Interfaces

3 interfaces between chains.

A–D · 484 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 88 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 64 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3QAY · Catalytic domain of CD27L endolysin targeting Clostridia Difficile · 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 B6SBV8
Elsewhere: RCSB PDB 3QAY · PDBe 3QAY · UniProt B6SBV8

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