Research workbench

Cationic trypsin in complex with mutated spinacia oleracea trypsin inhibitor III (soti-III) (F14A)

Analyse Cationic trypsin in complex with mutated spinacia oleracea trypsin inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4AOQ
Type: protein
Length: 773 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cationic trypsin; Trypsin inhibitor 3
EC: 3.4.21.4
UniProt: P00760, P84781
Ligands: CA
Pockets: 5 · best druggability 0.59

Structure

x-ray diffraction · 3 distinct chains · 10% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Cationic trypsin (EC 3.4.21.4)	protein	223	10% helix, 35% strand	P00760
D	Trypsin inhibitor 3	protein	34	9% helix, 32% strand	P84781
E, F	Trypsin inhibitor 3	protein	35	9% helix, 31% strand	P84781

Ligands and binding sites

CA · Calcium ion · metal · 3 copies · chains A, B, C
1PE · Pentaethylene glycol · additive · chains B, E

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	439	0.59	0.75	48	empty
2	177	0.56	0.80	44	empty
3	58	0.52	0.87	24	empty
4	143	0.42	0.75	29	empty
5	83	0.36	0.76	18	empty

Interfaces

6 interfaces between chains.

B–E · 823 Å² buried · 19 hydrogen bonds · protein-protein
A–D · 799 Å² buried · 19 hydrogen bonds · protein-protein
C–F · 797 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 522 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 453 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 27 disulfide (disulfide).

Compared structures

4AOQ · Cationic trypsin in complex with mutated Spinacia oleracea trypsin inhibitor III… · the same entry in another collection · chain E against E, TM-score 1.00
1TNG · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain A against A, TM-score 1.00
1TNK · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain A against A, TM-score 1.00
1TNJ · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain A against A, TM-score 1.00
1TNH · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain A against A, TM-score 1.00
1TNL · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain A against A, TM-score 1.00

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 P00760
Every structure of UniProt P84781
Elsewhere: RCSB PDB 4AOQ · PDBe 4AOQ · UniProt P00760 · UniProt P84781

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