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Structure of mutant rip from barley seeds

Analyse Structure of mutant rip from barley seeds in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4FB9
Type: protein
Length: 1,114 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein synthesis inhibitor I
EC: 3.2.2.22
UniProt: P22244
Pockets: 19 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Protein synthesis inhibitor I (EC 3.2.2.22)	protein	278	39% helix, 16% strand	P22244
C, D	Protein synthesis inhibitor I (EC 3.2.2.22)	protein	279	39% helix, 15% strand	P22244

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1058	0.74	0.77	73	empty
2	999	0.73	0.76	65	empty
3	195	0.56	0.80	34	empty
4	172	0.51	0.78	32	empty
5	193	0.51	0.77	32	empty

Interfaces

5 interfaces between chains.

A–B · 838 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 812 Å² buried · 16 hydrogen bonds · protein-protein
A–D · 450 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 447 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 40 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 modified (engineered).

Compared structures

4FB9 · Structure of mutant RIP from barley seeds · the same entry in another collection · chain A against A, TM-score 1.00
P22244 · AlphaFold monomer V2.0 prediction for protein synthesis inhibitor I (P22244) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P22244
Elsewhere: RCSB PDB 4FB9 · PDBe 4FB9 · UniProt P22244

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