MolNFT v1 · #96229 · protein

Secreted chlamydial protein PGP3, coiled-coil deletion

4JDO · Virulence plasmid protein PGP3-D: “Secreted chlamydial protein PGP3, coiled-coil deletion”. X-ray diffraction, 1 ligand (NA), 20 pockets (best druggability 0.85). MolNFT v1 #96229 on GenesisL1: 3D structure, binding sites and…

PDB: 4JDO
Type: protein
Length: 1,949 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Virulence plasmid protein PGP3-D
UniProt: A0A0E9CJA7
Ligands: NA
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 6 distinct chains · 1% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Virulence plasmid protein PGP3-D	protein	215	1% helix, 54% strand	A0A0E9CJA7
B	Virulence plasmid protein PGP3-D	protein	218	1% helix, 53% strand	A0A0E9CJA7
C, F, G, I	Virulence plasmid protein PGP3-D	protein	217	1% helix, 54% strand	A0A0E9CJA7
D	Virulence plasmid protein PGP3-D	protein	217	1% helix, 54% strand	A0A0E9CJA7
E	Virulence plasmid protein PGP3-D	protein	215	1% helix, 54% strand	A0A0E9CJA7
H	Virulence plasmid protein PGP3-D	protein	216	0% helix, 55% strand	A0A0E9CJA7

Ligands and binding sites

NA · Sodium ion · metal · 3 copies · chains A, B, C, D, E, F, G, H, I

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

Pockets

20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	285	0.85	0.95	36	empty
2	256	0.84	0.96	37	empty
3	236	0.84	0.96	35	empty
4	133	0.79	0.97	31	empty
5	81	0.76	0.98	23	empty

Interfaces

13 interfaces between chains.

B–C · 2730 Å² buried · 36 hydrogen bonds · protein-protein
E–F · 2715 Å² buried · 33 hydrogen bonds · protein-protein
H–I · 2703 Å² buried · 37 hydrogen bonds · protein-protein
G–I · 2638 Å² buried · 37 hydrogen bonds · protein-protein
A–B · 2623 Å² buried · 29 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 43 modified (engineered).

Compared structures

4JDO · Secreted chlamydial protein pgp3, coiled-coil deletion · 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 A0A0E9CJA7
Elsewhere: RCSB PDB 4JDO · PDBe 4JDO · UniProt A0A0E9CJA7

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