MolNFT v1 · #97911 · protein

The complex structure of RV3378C-Y51FY90F with substrate, tpp

4KT8 · Diterpene synthase: “The complex structure of RV3378C-Y51FY90F with substrate, tpp”. X-ray diffraction, 2 ligands (9AX, PO4), 2 pockets (best druggability 0.74). MolNFT v1 #97911 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 4KT8
Type: protein
Length: 289 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Diterpene synthase
EC: 3.1.7.9, 3.1.7.8
UniProt: O50407
Ligands: 9AX, PO4
Pockets: 2 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Diterpene synthase (EC 3.1.7.9, 3.1.7.8)	protein	289	49% helix, 14% strand	O50407

Ligands and binding sites

9AX · (2E)-3-methyl-5-[(1R,2S,8aS)-1,2,5,5-tetramethyl-1,2,3,5,6,7,8,8a-octahydronaphthalen-1-yl]pent-2-en-1-yl trihydrogen diphosphate · ligand · chains A
PO4 · Phosphate ion · ion · 3 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	393	0.74	0.84	33	9AX
2	101	0.39	0.76	24	empty

Compared structures

4KT8 · The complex structure of Rv3378c-Y51FY90F with substrate, TPP · 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 O50407
Elsewhere: RCSB PDB 4KT8 · PDBe 4KT8 · UniProt O50407

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