SMTL ID : 5vmd.1 (1 other biounit)

Crystal structure of UBR-box from UBR6 in a domain-swapping conformation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

7 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.21, H.56 Chain B: H.21, H.56 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:H.21, A:H.56, B:H.21, B:H.56 ZN.2: 4 residues within 4Å: Chain A: C.38, C.41 Chain B: C.61, G.64 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Metal complexes: A:C.38, A:C.41, B:C.61 ZN.3: 5 residues within 4Å: Chain A: C.41, C.45 Chain B: C.63, C.72, T.73 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Metal complexes: B:C.63, B:C.72, A:C.41, A:C.45 ZN.4: 4 residues within 4Å: Chain A: C.26, C.29, H.46, H.49 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.26, A:C.29, A:H.46, A:H.49 ZN.5: 5 residues within 4Å: Chain A: C.63, C.72, T.73 Chain B: C.41, C.45 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:C.63, A:C.72, B:C.41, B:C.45 ZN.10: 3 residues within 4Å: Chain A: C.61 Chain B: C.38, C.41 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Metal complexes: B:C.38, B:C.41, A:C.61 ZN.11: 4 residues within 4Å: Chain B: C.26, C.29, H.46, H.49 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.26, B:C.29, B:H.46, B:H.49

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

EDO.6: 3 residues within 4Å: Chain A: Y.10, I.12, Y.15 1 PLIP interactions: 1 interactions with chain A Water bridges: A:I.12 EDO.7: 7 residues within 4Å: Chain A: I.42, K.43, H.46, Q.47, G.48, H.49, V.51 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.43, A:G.48, A:H.49 EDO.8: 4 residues within 4Å: Chain A: H.21, D.22 Chain B: R.58, F.59 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.58, B:R.58, A:D.22, A:D.22 EDO.9: 4 residues within 4Å: Chain A: H.27, D.50, V.51, E.52 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.50 EDO.12: 7 residues within 4Å: Chain A: H.21, F.23, A.36 Chain B: H.56, D.57, R.58, F.60 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.57, B:F.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Munoz-Escobar, J. et al., Crystal structure of the UBR-box from UBR6/FBXO11 reveals domain swapping mediated by zinc binding. Protein Sci. (2017)

Release Date

2017-07-12

Peptides

F-box only protein 11: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

F-box only protein 11

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