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Crystal structure of autoprocessed form of Tk-subtilisin

Analyse Crystal structure of autoprocessed form of Tk-subtilisin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2Z2Y
Type: protein
Length: 766 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.89
Source: Thermococcus kodakarensis
Molecule: Tk-subtilisin
EC: 3.4.21.62
UniProt: P58502
Ligands: CA, ZN
Pockets: 6 · best druggability 0.70

Structure

x-ray diffraction · resolution 1.89 · 2 distinct chains · 27% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Tk-subtilisin (EC 3.4.21.62)	protein	318	29% helix, 20% strand	P58502
B, D	Tk-subtilisin (EC 3.4.21.62)	protein	65	18% helix, 43% strand	P58502

Ligands and binding sites

CA · Calcium ion · metal · 14 copies · chains A, C
ZN · Zinc ion · metal · 6 copies · chains A, B, C, D

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

Pockets

6 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	341	0.70	0.83	43	empty
2	647	0.67	0.76	73	empty
3	59	0.66	0.94	17	empty
4	81	0.34	0.75	12	empty
5	67	0.33	0.76	14	empty

Interfaces

4 interfaces between chains.

A–B · 1114 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 1103 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 524 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 180 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

2Z2Y · Crystal structure of autoprocessed form of tk-subtilisin · the same entry in another collection · chain A against A, TM-score 1.00
P58502 · AlphaFold monomer V2.0 prediction for tk-subtilisin (P58502) · 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 P58502
Elsewhere: RCSB PDB 2Z2Y · PDBe 2Z2Y · UniProt P58502

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