SMTL ID : 5jnb.1

structure of GLD-2/RNP-8 complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

hetero-4-4-mer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: S.52, N.59, S.62, K.158, S.176 Ligands: MG.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.52, A:N.59, A:S.176 Salt bridges: A:K.158 SO4.6: 5 residues within 4Å: Chain B: S.52, N.59, S.62, K.158, S.176 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.52, B:N.59, B:N.59, B:S.176 Salt bridges: B:K.158 SO4.11: 6 residues within 4Å: Chain C: S.52, N.59, S.62, K.158, S.176 Ligands: EDO.13 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.52, C:N.59, C:N.59, C:S.176 Salt bridges: C:K.158 SO4.14: 5 residues within 4Å: Chain D: S.52, N.59, S.62, K.158, S.176 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.52, D:N.59, D:S.62, D:S.176, D:S.176 Salt bridges: D:K.158

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: S.52, D.65 Chain F: T.1 Ligands: SO4.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.65 MG.10: 3 residues within 4Å: Chain B: S.52, D.65 Chain E: T.1 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.65

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

EDO.3: 5 residues within 4Å: Chain A: N.170, K.171, S.172 Chain B: Q.93, Q.101 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.172, B:Q.101, B:Q.101 EDO.4: 7 residues within 4Å: Chain A: K.107, F.278, R.280, S.281 Chain F: V.8, Q.9, Q.10 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain F Hydrogen bonds: A:K.107, A:R.280, A:S.281, F:Q.9, F:Q.10 EDO.5: 9 residues within 4Å: Chain A: G.51, N.55, A.133, N.136, T.137, L.140, Y.177 Chain F: T.1, L.2 4 PLIP interactions: 1 interactions with chain F, 3 interactions with chain A Hydrogen bonds: F:L.2, A:N.55, A:N.136, A:T.137 EDO.7: 5 residues within 4Å: Chain B: V.83, N.86 Chain F: V.8, S.12, F.14 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain F Hydrogen bonds: B:N.86, F:S.12, F:S.12 EDO.8: 9 residues within 4Å: Chain B: G.51, N.55, A.133, N.136, T.137, L.140, Y.177 Chain E: T.1, L.2 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:G.51, B:N.55, B:N.136, B:T.137, E:L.2 EDO.9: 7 residues within 4Å: Chain B: K.107, F.278, R.280, S.281 Chain E: V.8, Q.9, Q.10 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain E Hydrogen bonds: B:K.107, B:S.281, E:Q.9, E:Q.10, E:Q.10 EDO.12: 7 residues within 4Å: Chain C: G.51, N.55, A.133, N.136, T.137, L.140 Ligands: EDO.13 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.51, C:N.55, C:A.133 Water bridges: C:N.136 EDO.13: 8 residues within 4Å: Chain C: S.52, N.55, K.158, S.176, Y.177, V.180 Ligands: SO4.11, EDO.12 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.55, C:K.158, C:K.158 EDO.15: 5 residues within 4Å: Chain D: G.51, N.55, N.136, T.137, Y.177 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.55, D:N.136

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakel, K. et al., Structural basis for the antagonistic roles of RNP-8 and GLD-3 in GLD-2 poly(A)-polymerase activity. Rna (2016)

Release Date

2016-06-22

Peptides

Poly(A) RNA polymerase gld-2: ABCD
RNP (RRM RNA binding domain) containing: EFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Poly(A) RNA polymerase gld-2

RNP (RRM RNA binding domain) containing