SMTL ID : 6jwi.2 (1 other biounit)

Yeast Npl4 in complex with Lys48-linked diubiquitin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

monomer

Ligands

6 x GLC- GLC: alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC.1: 12 residues within 4Å: Chain A: D.187, G.188, L.189, T.190, M.191, D.192, F.219, L.246, E.247, I.249, M.250, R.253 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.191, A:D.192 GLC-GLC.2: 10 residues within 4Å: Chain A: A.10, V.11, E.14, Q.133, S.159, S.161, K.162, E.175, N.371, K.373 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.159, A:N.371 GLC-GLC.3: 7 residues within 4Å: Chain A: Y.163, N.165, F.363, P.364, N.365 Ligands: GLC-GLC.5, BCN.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.163, A:Y.163, A:N.165, A:N.365 GLC-GLC.4: 2 residues within 4Å: Chain A: D.19, L.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.19, A:L.21 GLC-GLC.5: 8 residues within 4Å: Chain A: K.134, S.135, E.136, N.139, F.363, T.366 Ligands: GLC-GLC.3, GLC-GLC.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.135, A:S.135, A:E.136 GLC-GLC.6: 7 residues within 4Å: Chain A: N.139, E.286, I.287, D.288, H.361, F.363 Ligands: GLC-GLC.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.287, A:I.287

2 x ZN: ZINC ION(Non-covalent)

ZN.7: 4 residues within 4Å: Chain A: C.97, H.101, C.109, C.112 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.97, A:H.101, A:C.109, A:C.112 ZN.8: 4 residues within 4Å: Chain A: C.30, H.32, C.38, C.41 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.30, A:H.32, A:C.38, A:C.41

4 x BCN: BICINE(Non-covalent)

BCN.9: 5 residues within 4Å: Chain A: L.29, K.31, C.38, E.39 Ligands: BCN.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.31, A:E.39, A:E.39 Salt bridges: A:E.39 BCN.10: 3 residues within 4Å: Chain A: N.165 Ligands: GLC-GLC.3, GLC-GLC.3 No protein-ligand interaction detected (PLIP) BCN.11: 3 residues within 4Å: Chain A: M.37, C.38 Ligands: BCN.9 No protein-ligand interaction detected (PLIP) BCN.12: 3 residues within 4Å: Chain A: C.234, K.235, H.237 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.234

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sato, Y. et al., Structural insights into ubiquitin recognition and Ufd1 interaction of Npl4. Nat Commun (2019)

Release Date

2019-12-25

Peptides

Nuclear protein localization protein 4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

Nuclear protein localization protein 4

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