SMTL ID : 4k1r.3 (2 other biounits)

Crystal structure of Schizosaccharomyces pombe sst2 catalytic domain and Ubiquitin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

hetero-2-2-mer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.66, H.94, Q.190 Chain C: E.89 Ligands: CL.4 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Metal complexes: A:H.66, A:H.94, C:E.89, C:E.89 ZN.2: 5 residues within 4Å: Chain A: H.103, H.105, S.113, D.116 Chain B: G.81 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.103, A:H.105, A:D.116, A:D.116 ZN.3: 4 residues within 4Å: Chain A: H.118, C.159, H.166, H.168 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.118, A:C.159, A:H.166, A:H.168 ZN.11: 5 residues within 4Å: Chain C: H.103, H.105, S.113, D.116 Chain D: G.81 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.103, C:H.105, C:D.116, C:D.116 ZN.12: 4 residues within 4Å: Chain C: H.118, C.159, H.166, H.168 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.118, C:C.159, C:H.166, C:H.168 ZN.13: 5 residues within 4Å: Chain A: E.89 Chain C: H.66, H.94, Q.190 Ligands: CL.14 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Metal complexes: C:H.66, C:H.94, A:E.89, A:E.89

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

CL.4: 8 residues within 4Å: Chain A: H.66, F.90, H.94, Q.190, V.192 Chain C: E.89, F.90 Ligands: ZN.1 Ligand excluded by PLIP CL.14: 8 residues within 4Å: Chain A: E.89, F.90 Chain C: H.66, F.90, H.94, Q.190, V.192 Ligands: ZN.13 Ligand excluded by PLIP

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

EDO.5: 5 residues within 4Å: Chain A: Q.91, N.95, L.96, L.97 Chain B: L.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.91 EDO.6: 6 residues within 4Å: Chain A: H.105, Q.108, F.111, S.113, F.165 Chain B: G.81 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:Q.108, A:Q.108 Hydrogen bonds: B:G.81 EDO.7: 3 residues within 4Å: Chain A: T.107, S.138, K.139 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.138, A:K.139 EDO.8: 6 residues within 4Å: Chain A: K.32, S.142, G.143, I.144, Q.178, E.184 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.32, A:S.142, A:Q.178, A:Q.178 EDO.9: 2 residues within 4Å: Chain A: K.56, R.58 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.58, A:R.58 EDO.10: 6 residues within 4Å: Chain A: T.98 Chain B: T.12, L.13, L.74, V.75, L.76 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.98, A:T.98, B:L.13, B:L.76 EDO.15: 2 residues within 4Å: Chain C: T.75, D.77 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.75 EDO.16: 7 residues within 4Å: Chain C: Q.91, N.95, L.96, L.97 Chain D: K.11, T.12, L.13 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:Q.91 Water bridges: D:K.11, D:K.11, D:G.15 EDO.17: 6 residues within 4Å: Chain C: S.114, V.115, H.118, G.163, L.164, H.166 No protein-ligand interaction detected (PLIP) EDO.18: 6 residues within 4Å: Chain C: T.98 Chain D: T.12, L.13, L.74, V.75, L.76 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:L.13, D:L.76 Water bridges: D:L.76, C:T.98, C:T.98, C:Y.123

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shrestha, R.K. et al., Insights into the Mechanism of Deubiquitination by JAMM Deubiquitinases from Cocrystal Structures of the Enzyme with the Substrate and Product. Biochemistry (2014)

Release Date

2014-04-23

Peptides

AMSH-like protease sst2: AC
Polyubiquitin-C: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

AMSH-like protease sst2

Polyubiquitin-C

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