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Crystal structure of peps from streptococcus pneumoniae in complex with a substrate

Analyse Crystal structure of peps from streptococcus pneumoniae in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4ICS
Type: protein
Length: 830 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aminopeptidase peps
EC: 3.4.11.-
UniProt: Q97SP8
Ligands: ZN
Pockets: 13 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Aminopeptidase peps (EC 3.4.11.-)	protein	415	37% helix, 25% strand	Q97SP8

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B

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

Pockets

13 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	275	0.75	0.88	43	empty
2	254	0.75	0.88	36	empty
3	139	0.68	0.89	25	empty
4	133	0.66	0.88	32	empty
5	74	0.40	0.79	17	empty

Interfaces

1 interface between chains.

A–B · 1600 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

4ICS · Crystal structure of PepS from Streptococcus pneumoniae in complex with a substrate · 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 Q97SP8
Elsewhere: RCSB PDB 4ICS · PDBe 4ICS · UniProt Q97SP8

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