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Crystal structure of human senescence marker protein-30 (zinc bound)

Analyse Crystal structure of human senescence marker protein-30 (zinc bound) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3G4H
Type: protein
Length: 594 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Regucalcin
UniProt: Q15493
Ligands: ZN
Pockets: 4 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, A	Regucalcin	protein	297	4% helix, 53% strand	Q15493

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains B, A

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

Pockets

4 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	111	0.79	0.98	29	empty
2	103	0.77	0.98	24	empty
3	904	0.75	0.79	90	empty
4	151	0.44	0.76	26	empty

Interfaces

1 interface between chains.

B–A · 470 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

3G4H · Crystal structure of Human Senescence Marker Protein-30 (Zinc Bound) · the same entry in another collection · chain B against B, TM-score 1.00
Q15493 · AlphaFold monomer V2.0 prediction for regucalcin (Q15493) · 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 Q15493
Elsewhere: RCSB PDB 3G4H · PDBe 3G4H · UniProt Q15493

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