SMTL ID : 2wjv.1 (1 other biounit)

Crystal structure of the complex between human nonsense mediated decay factors UPF1 and UPF2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

hetero-1-1-mer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.9, C.12, C.31, H.41 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.9, A:C.12, A:C.31, A:H.41 ZN.2: 4 residues within 4Å: Chain A: C.23, S.26, H.45, C.51 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.23, A:S.26, A:H.45, A:C.51 ZN.3: 4 residues within 4Å: Chain A: C.69, C.72, C.95, C.99 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.69, A:C.72, A:C.95, A:C.99

13 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 4 residues within 4Å: Chain A: G.383, K.384, T.385, V.386 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.385, A:T.385, A:V.386 SO4.5: 3 residues within 4Å: Chain A: G.787, P.788, R.793 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.793 SO4.6: 5 residues within 4Å: Chain A: M.243, S.409, N.410, I.411, R.435 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.410, A:I.411 Salt bridges: A:R.435 SO4.7: 7 residues within 4Å: Chain A: G.378, P.380, G.381, Q.551, R.589, G.717, R.751 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.381, A:Q.551, A:G.717 Salt bridges: A:R.589, A:R.751 SO4.8: 5 residues within 4Å: Chain A: Y.650, R.729, H.733, Q.734, G.735 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.732, A:Q.734, A:G.735 Salt bridges: A:R.729 SO4.9: 1 residues within 4Å: Chain A: R.653 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.653 SO4.10: 2 residues within 4Å: Chain A: R.718, E.719 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.719 Salt bridges: A:R.718, A:K.720 SO4.11: 2 residues within 4Å: Chain A: N.358, H.359 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.359, A:S.360 Salt bridges: A:H.359 SO4.12: 4 residues within 4Å: Chain A: R.348, F.349, T.350, V.362 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.349, A:T.350, A:T.350 Salt bridges: A:R.348 SO4.13: 8 residues within 4Å: Chain A: T.680, P.681, S.711, V.712, D.713, G.737, F.738, R.744 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.712, A:D.713, A:D.713, A:F.738 Salt bridges: A:R.744 SO4.14: 5 residues within 4Å: Chain A: S.649, P.681, Y.682, E.683, I.736 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.683 SO4.15: 3 residues within 4Å: Chain A: T.304, R.308, P.509 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.308 SO4.16: 7 residues within 4Å: Chain A: L.430, C.431, A.432, E.436, L.447, H.448, R.510 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:C.431, A:E.436, A:H.448 Salt bridges: A:H.448, A:R.510

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Clerici, M. et al., Unusual Bipartite Mode of Interaction between the Nonsense-Mediated Decay Factors, Upf1 and Upf2. Embo J. (2009)

Release Date

2009-07-07

Peptides

REGULATOR OF NONSENSE TRANSCRIPTS 1: A
REGULATOR OF NONSENSE TRANSCRIPTS 2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

REGULATOR OF NONSENSE TRANSCRIPTS 1

REGULATOR OF NONSENSE TRANSCRIPTS 2

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