MolNFT v1 · #135327 · protein

Computationally designed fentanyl binder - FEN49* apo

5TVV · Endo-1,4-beta-xylanase a: “Computationally designed fentanyl binder - FEN49* apo”. X-ray diffraction, 1 ligand (K), 4 pockets (best druggability 0.77). MolNFT v1 #135327 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5TVV
Type: protein
Length: 554 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: K
Pockets: 4 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 5% helix, 65% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Endo-1,4-beta-xylanase a (EC 3.2.1.8)	protein	185	5% helix, 66% strand	P18429
C	Endo-1,4-beta-xylanase a (EC 3.2.1.8)	protein	184	5% helix, 64% strand	P18429

Ligands and binding sites

K · Potassium ion · metal · 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	970	0.77	0.79	79	empty
2	610	0.67	0.77	54	empty
3	273	0.58	0.77	33	empty
4	69	0.34	0.77	18	empty

Interfaces

3 interfaces between chains.

A–B · 480 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 405 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 14 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5TVV · Computationally Designed Fentanyl Binder - Fen49* Apo · 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 C 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 5TVV · PDBe 5TVV · UniProt P18429

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