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Structure of a malarial protein involved in proteostasis

Analyse Structure of a malarial protein involved in proteostasis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4XBI
Type: protein
Length: 745 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Clpb protein, PUTATIVE,GREEN fluorescent protein
UniProt: Q8IB03, P42212
Ligands: CRO, SO4
Pockets: 10 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 32% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Clpb protein, PUTATIVE,GREEN fluorescent protein	protein	376	31% helix, 33% strand	Q8IB03, P42212
B	Clpb protein, PUTATIVE,GREEN fluorescent protein	protein	369	32% helix, 33% strand	Q8IB03, P42212

Ligands and binding sites

CRO · {2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 5 copies · chains A, B

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

Pockets

10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	114	0.79	0.98	27	CRO
2	103	0.78	0.98	26	CRO
3	350	0.59	0.76	48	empty
4	308	0.52	0.74	40	empty
5	97	0.48	0.81	21	empty

Interfaces

1 interface between chains.

A–B · 712 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 cofactor (chromophore).

Compared structures

4XBI · Structure Of A Malarial Protein Involved in Proteostasis · the same entry in another collection · chain A against A, TM-score 1.00
P42212 · AlphaFold monomer V2.0 prediction for green fluorescent protein (P42212) · a predicted model of the same protein · chain B against A, TM-score 0.61

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 Q8IB03
Every structure of UniProt P42212
Elsewhere: RCSB PDB 4XBI · PDBe 4XBI · UniProt Q8IB03 · UniProt P42212

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