SMTL ID : 7mnk.1

Crystal structure of the tetramerization element of NUP358/RanBP2 (residues 805-832)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.10 Å

Oligo State

homo-tetramer

Ligands

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 4 residues within 4Å: Chain A: S.1, D.4 Chain D: K.27, S.30 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:K.27, D:S.30, A:S.1 Water bridges: A:S.1 EDO.2: 5 residues within 4Å: Chain A: K.20, Q.24 Chain B: E.17 Ligands: SO4.3, SO4.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.20 Water bridges: A:Q.24, A:Q.24 EDO.7: 4 residues within 4Å: Chain B: S.30 Chain C: S.1, Y.2, E.3 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.2 EDO.9: 7 residues within 4Å: Chain C: Y.2, N.6, L.9 Chain D: L.26, K.27, L.28, N.29 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:L.28, D:N.29, D:N.29

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

SO4.3: 7 residues within 4Å: Chain A: E.17, K.20, K.21, Q.24 Chain B: K.20 Ligands: EDO.2, SO4.5 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Water bridges: B:K.20, B:K.20 Salt bridges: B:K.20, A:K.20, A:K.21 SO4.4: 3 residues within 4Å: Chain A: K.27 Chain B: N.6, K.10 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.6 Salt bridges: B:K.10, A:K.27 Water bridges: A:K.27 SO4.5: 6 residues within 4Å: Chain A: K.20 Chain B: E.17, K.20, K.21 Ligands: EDO.2, SO4.3 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.17 Water bridges: B:K.20 Salt bridges: B:K.20, A:K.20 SO4.6: 2 residues within 4Å: Chain B: S.7, K.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.7 Salt bridges: B:K.10 SO4.8: 4 residues within 4Å: Chain C: E.17, K.20, K.21 Chain D: K.20 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:E.17 Water bridges: C:K.20 Salt bridges: C:K.20, D:K.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bley, C.J. et al., Architecture of the cytoplasmic face of the nuclear pore. Science (2022)

Release Date

2022-06-15

Peptides

E3 SUMO-protein ligase RanBP2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E3 SUMO-protein ligase RanBP2