MolNFT v1 · #84626 · protein

Prgi-sipd from salmonella typhimurium in complex with deoxycholate

3ZQE · Protein prgi, cell invasion protein sipd: “Prgi-sipd from salmonella typhimurium in complex with deoxycholate”. X-ray diffraction, 1 ligand (DXC), 5 pockets (best druggability 0.78). MolNFT v1 #84626 on GenesisL1: 3D structure…

PDB: 3ZQE
Type: protein
Length: 520 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein prgi, cell invasion protein sipd
UniProt: P41784, Q56026
Ligands: DXC
Pockets: 5 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 70% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein prgi, cell invasion protein sipd	protein	272	70% helix, 7% strand	P41784, Q56026
B	Protein prgi, cell invasion protein sipd	protein	248	71% helix, 10% strand	P41784, Q56026

Ligands and binding sites

DXC · (3alpha,5beta,12alpha)-3,12-dihydroxycholan-24-oic acid · ligand · chains A, B
GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

5 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	943	0.78	0.80	91	GOL
2	126	0.41	0.75	21	DXC
3	92	0.36	0.75	19	empty
4	59	0.29	0.74	15	empty
5	64	0.27	0.73	16	empty

Interfaces

1 interface between chains.

A–B · 1559 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

3ZQE · PrgI-SipD from Salmonella typhimurium in complex with deoxycholate · the same entry in another collection · chain A against A, TM-score 1.00
Q56026 · AlphaFold monomer V2.0 prediction for cell invasion protein sipd (Q56026) · a predicted model of the same protein · chain B against A, TM-score 0.78
P41784 · AlphaFold monomer V2.0 prediction for protein prgi (P41784) · a predicted model of the same protein · chain A against A, TM-score 0.24

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 P41784
Every structure of UniProt Q56026
Elsewhere: RCSB PDB 3ZQE · PDBe 3ZQE · UniProt P41784 · UniProt Q56026

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