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Chlamydia protein PGP3 studied at high resolution in a new crystal form

Analyse Chlamydia protein PGP3 studied at high resolution in a new crystal form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6GJT
Type: protein
Length: 1,059 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Virulence plasmid protein PGP3-D
UniProt: P0CE18
Ligands: K, BR
Pockets: 13 · best druggability 0.78

Structure

x-ray diffraction · 6 distinct chains · 4% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Virulence plasmid protein PGP3-D	protein	179	6% helix, 49% strand	P0CE18
B	Virulence plasmid protein PGP3-D	protein	178	6% helix, 49% strand	P0CE18
C	Virulence plasmid protein PGP3-D	protein	169	2% helix, 52% strand	P0CE18
D	Virulence plasmid protein PGP3-D	protein	177	2% helix, 49% strand	P0CE18
E	Virulence plasmid protein PGP3-D	protein	181	6% helix, 49% strand	P0CE18
F	Virulence plasmid protein PGP3-D	protein	175	2% helix, 50% strand	P0CE18

Ligands and binding sites

K · Potassium ion · metal · 6 copies · chains A, B, C, D, E, F
BR · Bromide ion · ion · 28 copies · chains A, B, C, E, D, F

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

Pockets

13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	125	0.78	0.97	30	BR
2	114	0.78	0.97	29	BR
3	99	0.75	0.96	27	empty
4	86	0.73	0.95	21	BR
5	51	0.69	0.98	20	empty

Interfaces

7 interfaces between chains.

D–E · 1609 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1569 Å² buried · 8 hydrogen bonds · protein-protein
D–F · 1498 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 1484 Å² buried · 13 hydrogen bonds · protein-protein
E–F · 1475 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

6GJT · Chlamydia protein Pgp3 studied at high resolution in a new crystal form · the same entry in another collection · chain F against F, TM-score 1.00
P0CE18 · AlphaFold monomer V2.0 prediction for virulence plasmid protein PGP3-D (P0CE18) · a predicted model of the same protein · chain B against A, TM-score 0.91

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 P0CE18
Elsewhere: RCSB PDB 6GJT · PDBe 6GJT · UniProt P0CE18

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