MolNFT v1 · #93566 · protein

Structural basis for allene oxide cyclization in moss

4H6B · Allene oxide cyclase: “Structural basis for allene oxide cyclization in moss”. X-ray diffraction, 3 ligands (10X, 10Y, PO4), 20 pockets (best druggability 0.73). MolNFT v1 #93566 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 4H6B
Type: protein
Length: 2,160 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Allene oxide cyclase
EC: 5.3.99.6
UniProt: Q8GS38
Ligands: 10X, 10Y, PO4
Pockets: 20 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, C, B, E, F, G, H, I, J, K, L	Allene oxide cyclase (EC 5.3.99.6)	protein	180	7% helix, 46% strand	Q8GS38

Ligands and binding sites

10X · (9Z)-11-{(2S,3S)-3-[(2Z)-pent-2-en-1-yl]oxiran-2-yl}undec-9-enoic acid · ligand · 3 copies · chains A, B, J
10Y · (9Z)-11-{(2R,3S)-3-[(2Z)-pent-2-en-1-yl]oxiran-2-yl}undec-9-enoic acid · ligand · 2 copies · chains A, G
PO4 · Phosphate ion · ion · 23 copies · chains A, D, C, B, E, F, G, H, I, J, K, L
HEZ · Hexane-1,6-diol · additive · 10 copies · chains D, E, C, B, G, F, I, H, K

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	902	0.73	0.77	80	HEZ, PO4
2	579	0.72	0.80	77	HEZ
3	116	0.69	0.90	23	10Y
4	134	0.68	0.89	22	10X
5	465	0.68	0.79	61	HEZ

Interfaces

19 interfaces between chains.

G–H · 890 Å² buried · 9 hydrogen bonds · protein-protein
B–F · 890 Å² buried · 8 hydrogen bonds · protein-protein
G–I · 882 Å² buried · 8 hydrogen bonds · protein-protein
K–L · 882 Å² buried · 8 hydrogen bonds · protein-protein
E–F · 880 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

4H6B · Structural basis for allene oxide cyclization in moss · 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 Q8GS38
Elsewhere: RCSB PDB 4H6B · PDBe 4H6B · UniProt Q8GS38

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