MolNFT v1 · #183905 · protein

Crystal structure of a shortened ipgc variant in complex with N-(2H-1, 3-benzodioxol-5-YLMETHYL)CYCLOPENTANAMINE

7O6S · Chaperone protein ipgc: “Crystal structure of a shortened ipgc variant in complex with N-(2H-1…”. X-ray diffraction, 3 ligands (45N, MG, CL), 6 pockets (best druggability 0.61). MolNFT v1 #183905 on GenesisL1: 3D structure, binding…

PDB: 7O6S
Type: protein
Length: 279 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chaperone protein ipgc
UniProt: P0A2U4
Ligands: 45N, MG, CL
Pockets: 6 · best druggability 0.61

Structure

x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Chaperone protein ipgc	protein	137	77% helix, 0% strand	P0A2U4
B	Chaperone protein ipgc	protein	142	78% helix, 0% strand	P0A2U4

Ligands and binding sites

45N · N-(1,3-benzodioxol-5-ylmethyl)cyclopentanamine · ligand · chains A, B
MG · Magnesium ion · metal · chains B
CL · Chloride ion · ion · 3 copies · chains A, B
DMS · Dimethyl sulfoxide · additive · 2 copies · chains A
PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, 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	221	0.61	0.81	24	45N
2	114	0.49	0.80	19	empty
3	138	0.48	0.78	19	empty
4	70	0.35	0.76	17	empty
5	62	0.32	0.75	11	DMS

Interfaces

1 interface between chains.

A–B · 863 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

7O6S · Crystal structure of a shortened IpgC variant in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
P0A2U4 · AlphaFold monomer V2.0 prediction for chaperone protein ipgc (P0A2U4) · a predicted model of the same protein · chain A against A, TM-score 0.92

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
Elsewhere: RCSB PDB 7O6S · PDBe 7O6S · UniProt P0A2U4

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