SMTL ID : 5m0i.1

Crystal structure of the nuclear complex with She2p and the ASH1 mRNA E3-localization element

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

hetero-4-3-mer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: Q.156, I.159, L.169, D.170, L.171, V.174 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.169, A:L.171 EDO.2: 5 residues within 4Å: Chain A: D.111, N.114, Y.115, D.145, Y.148 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.57, B:K.57, A:N.114, A:D.145 EDO.5: 5 residues within 4Å: Chain A: F.64 Chain B: E.172, Q.175, F.176, K.179 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.172 EDO.6: 3 residues within 4Å: Chain B: S.166, D.170, Q.175 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.175 EDO.7: 6 residues within 4Å: Chain A: Y.115 Chain B: T.53, I.56, K.57, K.60 Chain F: C.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.60 Water bridges: B:K.57, B:K.57 EDO.8: 6 residues within 4Å: Chain B: Q.156, I.159, L.169, D.170, L.171, V.174 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.171, B:L.171 EDO.9: 4 residues within 4Å: Chain B: D.111, N.114, D.145, Y.148 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.111, B:N.114, B:D.145 Water bridges: A:K.57 EDO.10: 9 residues within 4Å: Chain A: S.101, V.104, K.105, L.168, L.169 Chain B: P.98, S.101, M.102, K.105 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.105, B:P.98 EDO.12: 6 residues within 4Å: Chain C: D.111, N.114, Y.115, D.145, Y.148 Chain D: K.57 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:D.111, C:N.114, C:D.145, D:K.57, D:K.57 EDO.15: 6 residues within 4Å: Chain C: F.64, S.68, S.71 Chain D: D.170, Q.175, K.179 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:D.170, D:K.179, D:K.179, C:S.68, C:S.71 EDO.17: 4 residues within 4Å: Chain C: F.64 Chain D: F.176, K.179 Chain E: U.7 No protein-ligand interaction detected (PLIP)

6 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.3: 3 residues within 4Å: Chain A: S.120, E.124 Chain B: F.50 No protein-ligand interaction detected (PLIP) MG.11: 1 residues within 4Å: Chain B: Y.116 No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Chain C: E.124 No protein-ligand interaction detected (PLIP) MG.16: 3 residues within 4Å: Chain C: F.50 Chain D: S.120, E.124 No protein-ligand interaction detected (PLIP) MG.21: 2 residues within 4Å: Chain F: C.6, U.7 No protein-ligand interaction detected (PLIP) MG.22: 2 residues within 4Å: Chain F: U.7, G.8 No protein-ligand interaction detected (PLIP)

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 2 residues within 4Å: Chain A: D.170, Q.175 No protein-ligand interaction detected (PLIP) ACT.14: 6 residues within 4Å: Chain C: V.45, T.129, N.131, D.133, L.134, F.241 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:V.45, C:T.129 Hydrogen bonds: C:N.131, C:D.133 ACT.18: 3 residues within 4Å: Chain E: A.9, A.10, C.19 No protein-ligand interaction detected (PLIP) ACT.19: 3 residues within 4Å: Chain E: A.4, A.5, A.20 No protein-ligand interaction detected (PLIP) ACT.20: 3 residues within 4Å: Chain E: G.13, A.15, A.16 No protein-ligand interaction detected (PLIP) ACT.23: 3 residues within 4Å: Chain F: A.4, A.5, A.20 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Edelmann, F.T. et al., Molecular architecture and dynamics of ASH1 mRNA recognition by its mRNA-transport complex. Nat. Struct. Mol. Biol. (2017)

Release Date

2017-01-18

Peptides

SWI5-dependent HO expression protein 2: ABCD
SWI5-dependent HO expression protein 3: GHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
C

C
B

D
A

G
H

H
J

I
I

SWI5-dependent HO expression protein 2

SWI5-dependent HO expression protein 3