Research workbench

Wild type staphopain-staphostatin complex

Analyse Wild type staphopain-staphostatin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1Y4H
Type: protein
Length: 564 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cysteine protease; Cysteine protease inhibitor
EC: 3.4.22.-
UniProt: Q70UQ8, Q9EYW6
Ligands: SO4, CL
Pockets: 6 · best druggability 0.53

Structure

x-ray diffraction · 2 distinct chains · 20% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Cysteine protease (EC 3.4.22.-)	protein	173	25% helix, 32% strand	Q70UQ8
C, D	Cysteine protease inhibitor	protein	109	10% helix, 56% strand	Q9EYW6

Ligands and binding sites

SO4 · Sulfate ion · ion · 5 copies · chains A, B, C
CL · Chloride ion · ion · 4 copies · chains A, 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	159	0.53	0.80	30	empty
2	105	0.51	0.82	23	empty
3	51	0.47	0.86	14	empty
4	161	0.47	0.77	26	empty
5	110	0.47	0.80	19	empty

Interfaces

3 interfaces between chains.

A–C · 1202 Å² buried · 17 hydrogen bonds · protein-protein
B–D · 1172 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 631 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

1Y4H · Wild type staphopain-staphostatin complex · the same entry in another collection · chain A against A, TM-score 1.00
Q9EYW6 · AlphaFold monomer V2.0 prediction for staphostatin B (Q9EYW6) · a predicted model of the same protein · chain C 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 Q70UQ8
Every structure of UniProt Q9EYW6
Elsewhere: RCSB PDB 1Y4H · PDBe 1Y4H · UniProt Q70UQ8 · UniProt Q9EYW6

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