MolNFT v1 · #180724 · protein

Crystal structure of STAMBPL1 in complex with an engineered binder

7L97 · Amsh-like protease: “Crystal structure of STAMBPL1 in complex with an engineered binder”. X-ray diffraction, 3 ligands (ZN, SO4, UNX), 2 pockets (best druggability 0.53). MolNFT v1 #180724 on GenesisL1: 3D structure, binding sites…

PDB: 7L97
Type: protein
Length: 252 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Amsh-like protease; Ubiquitin variant
EC: 3.4.19.-
UniProt: Q96FJ0
Ligands: ZN, SO4, UNX
Pockets: 2 · best druggability 0.53

Structure

x-ray diffraction · 2 distinct chains · 25% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Amsh-like protease (EC 3.4.19.-)	protein	175	26% helix, 33% strand	Q96FJ0
B	Ubiquitin variant	protein	77	23% helix, 35% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A
SO4 · Sulfate ion · ion · 2 copies · chains A
UNX · Unknown atom or ion · ion · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · 2 copies · chains A, B

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	88	0.53	0.85	26	empty
2	64	0.29	0.74	13	empty

Interfaces

1 interface between chains.

A–B · 1272 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

7L97 · Crystal structure of STAMBPL1 in complex with an engineered binder · the same entry in another collection · chain A against A, TM-score 1.00
Q96FJ0 · AlphaFold monomer V2.0 prediction for amsh-like protease (Q96FJ0) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q96FJ0
Elsewhere: RCSB PDB 7L97 · PDBe 7L97 · UniProt Q96FJ0

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