MolNFT v1 · #24598 · protein

Crystal structure of the sorghum bicolor dhurrinase 1

1V02: “Crystal structure of the sorghum bicolor dhurrinase 1”. X-ray diffraction, 19 pockets (best druggability 0.73). MolNFT v1 #24598 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1V02
Type: protein
Length: 2,904 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dhurrinase
EC: 3.2.1.21
UniProt: Q41290
Pockets: 19 · best druggability 0.73

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, F	Dhurrinase (EC 3.2.1.21)	protein	484	44% helix, 17% strand	Q41290
E	Dhurrinase (EC 3.2.1.21)	protein	484	45% helix, 17% strand	Q41290

Pockets

19 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	969	0.73	0.76	100	empty
2	376	0.72	0.83	53	empty
3	352	0.71	0.83	45	empty
4	442	0.71	0.81	58	empty
5	637	0.70	0.78	68	empty

Interfaces

8 interfaces between chains.

A–B · 1085 Å² buried · 9 hydrogen bonds · protein-protein
E–F · 1070 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 1064 Å² buried · 7 hydrogen bonds · protein-protein
B–E · 520 Å² buried · 3 hydrogen bonds · protein-protein
B–F · 351 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

1V02 · Crystal structure of the Sorghum bicolor dhurrinase 1 · the same entry in another collection · chain A 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 Q41290
Elsewhere: RCSB PDB 1V02 · PDBe 1V02 · UniProt Q41290

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