MolNFT v1 · #65508 · protein

Crystal structure of ipgc in complex with the chaperone binding region of ipab

3GZ1 · Chaperone protein ipgc: “Crystal structure of ipgc in complex with the chaperone binding region of ipab”. X-ray diffraction, 5 pockets (best druggability 0.63). MolNFT v1 #65508 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 3GZ1
Type: protein
Length: 309 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chaperone protein ipgc; Invasin ipab
UniProt: P0A2U4, P18011
Pockets: 5 · best druggability 0.63

Structure

x-ray diffraction · 4 distinct chains · 70% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Chaperone protein ipgc	protein	144	75% helix, 0% strand	P0A2U4
B	Chaperone protein ipgc	protein	142	76% helix, 0% strand	P0A2U4
P	Invasin ipab	protein	13	0% helix, 0% strand	P18011
Q	Invasin ipab	protein	10	0% helix, 0% strand	P18011

Ligands and binding sites

GOL · Glycerol · additive · 3 copies · chains A, Q, B, P

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	173	0.63	0.84	24	empty
2	234	0.56	0.78	39	empty
3	120	0.48	0.79	25	empty
4	57	0.36	0.79	14	GOL
5	67	0.30	0.74	14	empty

Interfaces

3 interfaces between chains.

A–B · 1430 Å² buried · 6 hydrogen bonds · protein-protein
B–P · 628 Å² buried · 5 hydrogen bonds · protein-protein
A–Q · 573 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

3GZ1 · Crystal structure of IpgC in complex with the chaperone binding region of IpaB · the same entry in another collection · chain Q against Q, TM-score 1.00
P0A2U4 · AlphaFold monomer V2.0 prediction for chaperone protein ipgc (P0A2U4) · a predicted model of the same protein · chain B against A, TM-score 0.91
P18011 · AlphaFold monomer V2.0 prediction for invasin ipab (P18011) · a predicted model of the same protein · chain Q against A, TM-score 0.40

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 P0A2U4
Every structure of UniProt P18011
Elsewhere: RCSB PDB 3GZ1 · PDBe 3GZ1 · UniProt P0A2U4 · UniProt P18011

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