MolNFT v1 · #135458 · protein

Computationally designed fentanyl binder - FEN49*-complex

5TZO · Endo-1,4-beta-xylanase a: “Computationally designed fentanyl binder - FEN49*-complex”. X-ray diffraction, 3 ligands (7V7, K, CL), 4 pockets (best druggability 0.75). MolNFT v1 #135458 on GenesisL1: 3D structure, binding sites and…

PDB: 5TZO
Type: protein
Length: 555 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Endo-1,4-beta-xylanase a
EC: 3.2.1.8
UniProt: P18429
Ligands: 7V7, K, CL
Pockets: 4 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 66% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Endo-1,4-beta-xylanase a (EC 3.2.1.8)	protein	185	5% helix, 66% strand	P18429

Ligands and binding sites

7V7 · N-phenyl-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide · ligand · 6 copies · chains A, B, C
K · Potassium ion · metal · 3 copies · chains A, B
CL · Chloride ion · ion · 3 copies · chains A, B, C

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	1094	0.75	0.77	88	7V7, CL
2	370	0.68	0.80	36	7V7, CL
3	312	0.67	0.81	34	7V7, CL
4	114	0.44	0.78	18	empty

Interfaces

3 interfaces between chains.

B–C · 527 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 455 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 143 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5TZO · Computationally Designed Fentanyl Binder - Fen49*-Complex · the same entry in another collection · chain A against A, TM-score 1.00
P18429 · AlphaFold monomer V2.0 prediction for endo-1,4-beta-xylanase a (P18429) · a predicted model of the same protein · chain A 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 P18429
Elsewhere: RCSB PDB 5TZO · PDBe 5TZO · UniProt P18429

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