SMTL ID : 7l97.1

Crystal structure of STAMBPL1 in complex with an engineered binder

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

hetero-1-1-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.101, C.141, H.147, H.149 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.101, A:C.141, A:H.147, A:H.149 ZN.2: 3 residues within 4Å: Chain A: H.86, H.88, D.99 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.86, A:H.88, A:D.99, A:D.99

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 6 residues within 4Å: Chain A: L.5, R.129, I.158, C.159, K.160, H.161 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.160, A:H.161, A:H.161 EDO.7: 6 residues within 4Å: Chain A: T.81 Chain B: T.8, L.9, L.70, V.71, L.72 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.9, B:L.72, A:T.81

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 4 residues within 4Å: Chain A: T.125, G.126, I.127, I.158 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.127 SO4.5: 3 residues within 4Å: Chain A: T.150, K.151, E.152 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.151, A:E.152, A:E.152

2 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.6: 2 residues within 4Å: Chain A: C.159, V.162 No protein-ligand interaction detected (PLIP) UNX.8: 1 residues within 4Å: Chain B: E.17 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, Y. et al., Structural and functional characterization of ubiquitin variant inhibitors for the JAMM-family deubiquitinases STAMBP and STAMBPL1. J.Biol.Chem. (2021)

Release Date

2021-08-25

Peptides

AMSH-like protease: A
Ubiquitin variant: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

AMSH-like protease

Ubiquitin variant