MolNFT v1 · #51785 · protein

Cathsilicatein, a chimera

2VHS: “Cathsilicatein, a chimera”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.77). MolNFT v1 #51785 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2VHS
Type: protein
Length: 860 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cathsilicatein
UniProt: P07711
Ligands: SO4
Pockets: 6 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 28% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Cathsilicatein	protein	215	28% helix, 23% strand	P07711

Ligands and binding sites

SO4 · Sulfate ion · ion · 8 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1072	0.77	0.79	109	SO4
2	560	0.74	0.81	58	SO4
3	137	0.42	0.75	28	empty
4	83	0.37	0.76	14	empty
5	78	0.33	0.74	16	empty

Interfaces

4 interfaces between chains.

A–B · 781 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 765 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 346 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 343 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

2VHS · Cathsilicatein, a chimera · the same entry in another collection · chain D against D, TM-score 1.00
P07711 · AlphaFold monomer V2.0 prediction for procathepsin L (P07711) · a predicted model of the same protein · chain B 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 P07711
Elsewhere: RCSB PDB 2VHS · PDBe 2VHS · UniProt P07711

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