SMTL ID : 6ml1.3 (2 other biounits)

Structure of the USP15 deubiquitinase domain in complex with an affinity-matured inhibitory Ubv

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-2-2-1-mer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.279, Q.345 Chain B: D.279, Q.345 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.279, A:D.279, A:D.279, H2O.2, H2O.8 CA.2: 3 residues within 4Å: Chain A: C.285, R.344 Chain E: H.4 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: A:C.285, E:H.4, H2O.6, H2O.15 CA.6: 3 residues within 4Å: Chain B: E.181, E.235, Q.237 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.181, B:E.235 CA.12: 2 residues within 4Å: Chain D: K.36, E.37 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:K.36

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.179, C.182, C.230, C.233 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.179, A:C.182, A:C.230, A:C.233 ZN.7: 4 residues within 4Å: Chain B: C.179, C.182, C.230, C.233 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.179, B:C.182, B:C.230, B:C.233

4 x NA: SODIUM ION(Non-functional Binders)

NA.4: 2 residues within 4Å: Chain A: L.63, G.64 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.63 NA.5: 5 residues within 4Å: Chain A: K.208, L.209, K.210, D.274, P.276 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.209, A:K.210, A:D.274 NA.10: 5 residues within 4Å: Chain B: K.208, L.209, K.210, D.274, P.276 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.209, B:K.210, B:D.274 NA.11: 4 residues within 4Å: Chain B: P.198, L.199, K.257, S.260 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.199, B:S.260, B:S.260

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

EDO.8: 5 residues within 4Å: Chain B: D.281, G.284, C.285, R.286, S.348 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.348, B:S.348 Water bridges: B:G.284

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 2 residues within 4Å: Chain A: Q.345 Chain B: N.278 Ligand excluded by PLIP

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.13: 4 residues within 4Å: Chain D: N.28, A.31, K.32, D.35 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.35 Salt bridges: D:D.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Teyra, J. et al., Structural and Functional Characterization of Ubiquitin Variant Inhibitors of USP15. Structure (2019)

Release Date

2019-01-23

Peptides

Ubiquitin carboxyl-terminal hydrolase 15,Ubiquitin carboxyl-terminal hydrolase 15,Ubiquitin carboxyl-terminal hydrolase 15: AB
Ubiquitin variant 15.1a: CD
Proteolyzed N-terminal tag of Ubv.15.1a construct: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

D
C

E
G

Ubiquitin carboxyl-terminal hydrolase 15,Ubiquitin carboxyl-terminal hydrolase 15,Ubiquitin carboxyl-terminal hydrolase 15

Ubiquitin variant 15.1a

Proteolyzed N-terminal tag of Ubv.15.1a construct

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