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Cap domain of enterococcal prga

Analyse Cap domain of enterococcal prga in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6Z9K
Type: protein
Length: 488 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Prga
UniProt: Q04111
Ligands: MG
Pockets: 6 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Prga	protein	239	45% helix, 14% strand	Q04111
B	Prga	protein	249	48% helix, 13% strand	Q04111

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, B
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1010	0.80	0.81	97	empty
2	158	0.50	0.78	23	empty
3	93	0.40	0.77	15	MG
4	145	0.39	0.73	19	empty
5	129	0.39	0.74	19	empty

Interfaces

1 interface between chains.

A–B · 587 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

6Z9K · CAP domain of Enterococcal PrgA · 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 Q04111
Elsewhere: RCSB PDB 6Z9K · PDBe 6Z9K · UniProt Q04111

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