SMTL ID : 5d1k.1

Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: Y.74, I.137, W.141 Ligands: OXL.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.141 EDO.6: 2 residues within 4Å: Chain B: E.122, R.123 No protein-ligand interaction detected (PLIP) EDO.7: 2 residues within 4Å: Chain B: K.25, Y.29 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.25 Water bridges: B:Y.29, B:Y.29

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 5 residues within 4Å: Chain A: R.72, S.80, W.141, Y.145 Ligands: OXL.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.145

1 x OXL: OXALATE ION(Non-covalent)

OXL.3: 5 residues within 4Å: Chain A: W.141, K.144, Y.145 Ligands: EDO.1, PEG.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.141, A:W.141

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain B: C.10, C.13, H.33, C.36 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.10, B:C.13, B:H.33, B:C.36 ZN.5: 4 residues within 4Å: Chain B: C.28, H.30, C.73, C.76 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.28, B:H.30, B:C.73, B:C.76

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, S. et al., Insights into Ubiquitination from the Unique Clamp-like Binding of the RING E3 AO7 to the E2 UbcH5B. J.Biol.Chem. (2015)

Release Date

2015-10-28

Peptides

Ubiquitin-conjugating enzyme E2 D2: A
E3 ubiquitin-protein ligase RNF25: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ubiquitin-conjugating enzyme E2 D2

E3 ubiquitin-protein ligase RNF25

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