Research workbench

Human chymase - fynomer complex

Analyse Human chymase - fynomer complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4AG2
Type: protein
Length: 565 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chymase; Fynomer
EC: 3.4.21.39
UniProt: P23946
Ligands: LMR, NA
Pockets: 4 · best druggability 0.67

Structure

x-ray diffraction · 4 distinct chains · 8% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Chymase (EC 3.4.21.39)	protein	223	9% helix, 38% strand	P23946
B	Chymase (EC 3.4.21.39)	protein	226	8% helix, 38% strand	P23946
C	Fynomer	protein	58	5% helix, 47% strand	—
D	Fynomer	protein	58	5% helix, 47% strand	—

Ligands and binding sites

LMR · (2S)-2-hydroxybutanedioic acid · ligand · 3 copies · chains A, C, B, D
NA · Sodium ion · metal · 5 copies · chains A, C, D
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, C

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

Pockets

4 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	251	0.67	0.84	30	LMR
2	324	0.66	0.81	38	NA
3	67	0.32	0.75	15	empty
4	57	0.28	0.75	18	empty

Interfaces

2 interfaces between chains.

B–D · 961 Å² buried · 25 hydrogen bonds · protein-protein
A–C · 945 Å² buried · 25 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

4AG2 · Human Chymase - Fynomer Complex · the same entry in another collection · chain A against A, TM-score 1.00
P23946 · AlphaFold monomer V2.0 prediction for chymase (P23946) · a predicted model of the same protein · chain B 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 P23946
Elsewhere: RCSB PDB 4AG2 · PDBe 4AG2 · UniProt P23946

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