SMTL ID : 6jwj.1

Npl4 in complex with Ufd1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

hetero-1-1-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 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 ZN.2: 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

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: Y.163, D.164, T.166, P.167, L.168, G.169 Ligands: GOL.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.164, A:D.164, A:L.168, A:G.169 Water bridges: A:D.19, A:G.20 GOL.4: 6 residues within 4Å: Chain A: G.20, L.21, I.22, Y.51, P.167 Ligands: GOL.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.20, A:Y.51 GOL.5: 8 residues within 4Å: Chain A: E.140, T.378, G.379, F.380, P.381, W.382, R.385, Q.390 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.379, A:W.382, A:R.385, A:R.385 GOL.6: 3 residues within 4Å: Chain A: D.90, R.92, P.114 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.92 Water bridges: A:S.115 GOL.7: 5 residues within 4Å: Chain A: A.16, H.63, L.66, K.67, N.70 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.63, A:L.66, A:K.67, A:K.67, A:N.70 GOL.8: 6 residues within 4Å: Chain A: E.131, Q.133, S.161, K.171, V.173, N.371 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.133, A:S.161, A:S.161, A:K.171, A:E.175 Water bridges: A:K.162 GOL.9: 7 residues within 4Å: Chain A: H.52, E.53, I.57, K.58, H.59, I.60, E.123 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.60 Water bridges: A:H.59, A:E.123 GOL.10: 7 residues within 4Å: Chain A: I.289, S.290, S.291, T.358, L.359, T.360, H.361 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.291, A:S.291, A:S.291, A:L.359, A:H.361 GOL.11: 1 residues within 4Å: Chain A: R.106 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.106 GOL.12: 2 residues within 4Å: Chain B: P.22, M.23 No protein-ligand interaction detected (PLIP) GOL.13: 7 residues within 4Å: Chain A: L.246, I.249, M.250, R.253 Chain B: L.12, P.13, Q.16 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.12, B:Q.16, A:L.246 Water bridges: B:D.11, B:L.12, B:G.15

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
Peptide from Ubiquitin fusion degradation protein 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Nuclear protein localization protein 4

Peptide from Ubiquitin fusion degradation protein 1

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