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1.95 ångström resolution crystal structure of stage II sporulation protein D (spoiid) from clostridium difficile in apo conformation

Analyse 1.95 ångström resolution crystal structure of stage II sporulation protein D… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5TXU
Type: protein
Length: 285 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Stage II sporulation protein D
UniProt: Q18CL6
Ligands: NA, ZN, CL
Pockets: 1 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Stage II sporulation protein D	protein	285	36% helix, 24% strand	Q18CL6

Ligands and binding sites

NA · Sodium ion · metal · 2 copies · chains A
ZN · Zinc ion · metal · chains A
CL · Chloride ion · ion · chains A
FMT · Formic acid · additive · 16 copies · chains A
DMS · Dimethyl sulfoxide · additive · 5 copies · chains A

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	381	0.59	0.76	43	CL, FMT, DMS

Compared structures

5TXU · 1.95 Angstrom Resolution Crystal Structure of Stage II Sporulation Protein D (SpoIID)… · 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 Q18CL6
Elsewhere: RCSB PDB 5TXU · PDBe 5TXU · UniProt Q18CL6

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