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Crystal structure of mavicyanin from cucurbita pepo medullosa (zucchini)

Analyse Crystal structure of mavicyanin from cucurbita pepo medullosa (zucchini) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1WS8
Type: protein
Length: 413 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mavicyanin
UniProt: P80728
Ligands: CU
Pockets: 5 · best druggability 0.64

Structure

x-ray diffraction · 2 distinct chains · 14% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mavicyanin	protein	104	14% helix, 32% strand	P80728
B, C, D	Mavicyanin	protein	103	14% helix, 34% strand	P80728

Ligands and binding sites

CU · Copper (II) ion · metal · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 2 copies · chains A, D

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

Pockets

5 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	442	0.64	0.77	64	empty
2	297	0.60	0.78	34	empty
3	153	0.51	0.79	30	empty
4	75	0.32	0.75	20	empty
5	68	0.29	0.73	20	empty

Interfaces

5 interfaces between chains.

A–C · 347 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 341 Å² buried · 1 hydrogen bond · protein-protein
A–B · 340 Å² buried · 1 hydrogen bond · protein-protein
B–D · 300 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 243 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

1WS8 · Crystal Structure of Mavicyanin from Cucurbita pepo medullosa (Zucchini) · the same entry in another collection · chain A against A, TM-score 1.00
P80728 · AlphaFold monomer V2.0 prediction for mavicyanin (P80728) · 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 P80728
Elsewhere: RCSB PDB 1WS8 · PDBe 1WS8 · UniProt P80728

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