SMTL ID : 2nvu.1

Structure of APPBP1-UBA3~NEDD8-NEDD8-MgATP-Ubc12(C111A), a trapped ubiquitin-like protein activation complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-1-1-1-2-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain B: D.509 Ligands: ATP.3 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.509, H2O.2

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain B: C.562, C.565, C.706, C.709 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.562, B:C.565, B:C.706, B:C.709

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.3: 19 residues within 4Å: Chain A: R.17 Chain B: A.419, G.420, D.442, M.443, D.444, N.450, R.453, Q.454, K.466, N.488, K.489, I.490, Q.491, G.507, L.508, D.509 Chain D: G.81 Ligands: MG.1 23 PLIP interactions: 21 interactions with chain B, 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: B:A.419, B:M.443, B:D.444, B:D.444, B:D.444, B:D.444, B:N.450, B:Q.454, B:I.490, B:Q.491, D:G.81 Water bridges: B:R.453, B:R.453, B:K.466, B:K.466, B:S.510, B:I.652 Salt bridges: B:R.453, B:R.453, B:R.453, B:K.466, B:K.466, A:R.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, D.T. et al., Basis for a ubiquitin-like protein thioester switch toggling E1-E2 affinity. Nature (2007)

Release Date

2007-01-30

Peptides

NEDD8-activating enzyme E1 regulatory subunit: A
Maltose binding protein/NEDD8-activating enzyme E1 catalytic subunit chimera: B
NEDD8-conjugating enzyme Ubc12: C
NEDD8: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
I

E
J

NEDD8-activating enzyme E1 regulatory subunit

Maltose binding protein/NEDD8-activating enzyme E1 catalytic subunit chimera

NEDD8-conjugating enzyme Ubc12

NEDD8

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