Research workbench

Human cathepsin-G inhibited by S. aureus EAPH1

Analyse Human cathepsin-G inhibited by S. aureus EAPH1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6VTM
Type: protein
Length: 1,276 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cathepsin G; MAP domain-containing protein
EC: 3.4.21.20
UniProt: P08311, A0A0H3K0M1
Ligands: SO4
Pockets: 9 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 17% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D, G	Cathepsin G (EC 3.4.21.20)	protein	223	10% helix, 40% strand	P08311
B, E, F	MAP domain-containing protein	protein	96	26% helix, 44% strand	A0A0H3K0M1
H	MAP domain-containing protein	protein	96	26% helix, 44% strand	A0A0H3K0M1

Ligands and binding sites

SO4 · Sulfate ion · ion · 13 copies · chains A, C, G, D, E

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

Pockets

9 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	1102	0.84	0.85	141	SO4
2	1082	0.84	0.85	113	SO4
3	239	0.53	0.77	30	empty
4	161	0.47	0.77	22	empty
5	166	0.46	0.76	29	empty

Interfaces

15 interfaces between chains.

C–F · 1054 Å² buried · 23 hydrogen bonds · protein-protein
D–E · 1035 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 1021 Å² buried · 25 hydrogen bonds · protein-protein
G–H · 1006 Å² buried · 21 hydrogen bonds · protein-protein
A–D · 589 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

6VTM · Human Cathepsin-G Inhibited by S. aureus EapH1 · the same entry in another collection · chain H against H, TM-score 1.00
P08311 · AlphaFold monomer V2.0 prediction for cathepsin G (P08311) · a predicted model of the same protein · chain D 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 P08311
Every structure of UniProt A0A0H3K0M1
Elsewhere: RCSB PDB 6VTM · PDBe 6VTM · UniProt P08311 · UniProt A0A0H3K0M1

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