SMTL ID : 6tgs.1

AtNBR1-PB1 domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

monomer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: S.13, Y.14, G.15, G.16, N.88, V.89 Ligands: PEG.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.14, A:G.15, A:G.16, A:V.89 GOL.2: 8 residues within 4Å: Chain A: M.35, K.39, A.52, E.53, L.54, L.56, L.68, V.69 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.54 GOL.3: 5 residues within 4Å: Chain A: Y.58, V.66, D.73, D.76, Q.80 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.73, A:Q.80 GOL.4: 2 residues within 4Å: Chain A: R.19, L.45 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.19 GOL.5: 2 residues within 4Å: Chain A: D.51 Ligands: SIN.10 No protein-ligand interaction detected (PLIP)

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

PEG.6: 7 residues within 4Å: Chain A: S.13, G.16, V.17, L.18, K.86, N.88 Ligands: GOL.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.13, A:L.18, A:K.86, A:K.86

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

SO4.7: 3 residues within 4Å: Chain A: K.26, A.27, N.28 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.27, A:N.28, A:N.28 SO4.8: 1 residues within 4Å: Chain A: D.32 No protein-ligand interaction detected (PLIP)

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 1 residues within 4Å: Chain A: K.11 Ligand excluded by PLIP

1 x SIN: SUCCINIC ACID(Non-covalent)

SIN.10: 5 residues within 4Å: Chain A: A.36, K.39, E.40, A.50 Ligands: GOL.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.40, A:A.50 Hydrogen bonds: A:E.40, A:A.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jakobi, A.J. et al., Structural basis of p62/SQSTM1 helical filaments and their role in cellular cargo uptake. Nat Commun (2020)

Release Date

2020-02-12

Peptides

Protein NBR1 homolog: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Protein NBR1 homolog