SMTL ID : 3wup.2 (1 other biounit)

Crystal Structure of the Ubiquitin-Binding Zinc Finger (UBZ) Domain of the Human DNA Polymerase Eta

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-trimer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.8, C.11, H.23, H.27 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.8, A:C.11, A:H.23, A:H.27 ZN.5: 4 residues within 4Å: Chain B: C.8, C.11, H.23, H.27 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.8, B:C.11, B:H.23, B:H.27 ZN.9: 4 residues within 4Å: Chain C: C.8, C.11, H.23, H.27 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.8, C:C.11, C:H.23, C:H.27

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

CL.2: 5 residues within 4Å: Chain A: Y.26 Chain B: Y.26 Chain C: Y.26 Ligands: CL.6, CL.10 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain A: Y.26 Chain B: Y.26 Chain C: Y.26 Ligands: CL.2, CL.10 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain A: Y.26 Chain B: Y.26 Chain C: Y.26 Ligands: CL.2, CL.6 Ligand excluded by PLIP

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

NA.3: 5 residues within 4Å: Chain A: S.13 Chain B: S.13 Chain C: S.13 Ligands: NA.7, NA.11 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:S.13, C:S.13, A:S.13, A:S.13 NA.7: 5 residues within 4Å: Chain A: S.13 Chain B: S.13 Chain C: S.13 Ligands: NA.3, NA.11 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:S.13, C:S.13, A:S.13, A:S.13 NA.11: 5 residues within 4Å: Chain A: S.13 Chain B: S.13 Chain C: S.13 Ligands: NA.3, NA.7 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:S.13, C:S.13, A:S.13, A:S.13

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: P.21, M.24, D.25 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.21 GOL.8: 3 residues within 4Å: Chain B: P.21, M.24, D.25 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.21 GOL.12: 3 residues within 4Å: Chain C: P.21, M.24, D.25 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:P.21

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Suzuki, N. et al., A novel mode of ubiquitin recognition by the ubiquitin-binding zinc finger domain of WRNIP1. Febs J. (2016)

Release Date

2015-06-17

Peptides

DNA polymerase eta: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

DNA polymerase eta

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