SMTL ID : 9b12.2 (1 other biounit)

Structure of Optineurin bound to HOIP NZF1 domain and M1-linked diubiquitin, crystal form 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

hetero-2-1-2-mer

Ligands

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

CL.1: 3 residues within 4Å: Chain A: E.18 Chain B: K.13 Chain D: R.2 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain E: R.2, G.3 Ligand excluded by PLIP

3 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.2: 6 residues within 4Å: Chain B: D.29, K.32, Q.33, A.36 Chain E: S.9, R.26 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain B Hydrogen bonds: E:S.9 Salt bridges: B:D.29, B:D.29 EPE.3: 4 residues within 4Å: Chain C: E.127, R.130, D.134, Y.135 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.130 Water bridges: C:E.127 Salt bridges: C:E.127, C:R.130 EPE.8: 4 residues within 4Å: Chain E: L.20, C.21, S.22, E.25 1 PLIP interactions: 1 interactions with chain E Water bridges: E:L.20

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain D: C.7, C.10, C.21, C.24 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.7, D:C.10, D:C.21, D:C.24 ZN.5: 4 residues within 4Å: Chain E: C.7, C.10, C.21, C.24 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.7, E:C.10, E:C.21, E:C.24

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.6: 4 residues within 4Å: Chain E: R.4, F.12, E.13, E.15 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.4, E:R.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Michel, M.A. et al., Linkage and substrate specificity conferred by NZF ubiquitin binding domains. To Be Published

Release Date

2024-07-31

Peptides

Optineurin: AB
Ubiquitin: C
E3 ubiquitin-protein ligase RNF31: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
A

D
I

E
J

Optineurin

Ubiquitin

E3 ubiquitin-protein ligase RNF31

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