SMTL ID : 6qlb.1

Calpain small subunit 1, RNA-binding protein Hfq

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

hetero-4-4-mer

Ligands

20 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.57, D.59, T.61, K.63, E.68 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.57, A:D.59, A:T.61, A:E.68, H2O.1 CA.2: 5 residues within 4Å: Chain A: D.87, D.89, S.91, T.93, E.98 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.87, A:S.91, A:E.98, A:E.98, H2O.1 CA.3: 4 residues within 4Å: Chain A: D.42, D.130, D.132, N.133 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.42, A:D.130, A:D.132, H2O.1, H2O.1 CA.4: 4 residues within 4Å: Chain A: A.14, D.17, E.19, E.24 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:A.14, A:D.17, A:E.19, A:E.24, H2O.1 CA.5: 4 residues within 4Å: Chain A: D.152, N.154, T.156, Q.158 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.152, A:T.156, A:Q.158, H2O.1, H2O.2 CA.8: 4 residues within 4Å: Chain B: A.14, D.17, E.19, E.24 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:A.14, B:E.19, B:E.24, B:E.24, H2O.3 CA.9: 5 residues within 4Å: Chain B: D.57, D.59, T.61, K.63, E.68 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.57, B:D.59, B:T.61, B:K.63, H2O.2 CA.10: 5 residues within 4Å: Chain B: D.87, D.89, S.91, T.93, E.98 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.87, B:D.89, B:S.91, B:E.98, H2O.2 CA.11: 4 residues within 4Å: Chain B: D.42, D.130, D.132, N.133 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.42, B:D.130, B:D.132, H2O.1, H2O.3 CA.12: 4 residues within 4Å: Chain B: D.152, N.154, T.156, Q.158 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.156, B:Q.158, H2O.3 CA.15: 4 residues within 4Å: Chain C: A.14, D.17, E.19, E.24 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:A.14, C:D.17, C:E.19, C:E.24, H2O.4 CA.16: 4 residues within 4Å: Chain C: D.42, D.130, D.132, N.133 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.42, C:D.130, C:D.132, H2O.4, H2O.4 CA.17: 5 residues within 4Å: Chain C: D.57, D.59, T.61, K.63, E.68 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.57, C:D.59, C:T.61, C:K.63, H2O.4 CA.18: 5 residues within 4Å: Chain C: D.87, D.89, S.91, T.93, E.98 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.87, C:D.89, C:S.91, C:E.98, H2O.4 CA.19: 4 residues within 4Å: Chain C: D.152, N.154, T.156, Q.158 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.152, C:T.156, C:Q.158, H2O.4, H2O.4 CA.20: 5 residues within 4Å: Chain D: A.14, D.17, E.19, S.21, E.24 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:A.14, D:D.17, D:E.19, D:E.24, D:E.24 CA.21: 4 residues within 4Å: Chain D: D.42, D.130, D.132, N.133 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.42, D:D.130, D:D.132, H2O.5, H2O.5 CA.22: 6 residues within 4Å: Chain D: E.19, D.57, D.59, T.61, K.63, E.68 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.57, D:D.59, D:T.61, D:K.63, D:E.68 CA.23: 5 residues within 4Å: Chain D: D.87, D.89, S.91, T.93, E.98 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.87, D:D.89, D:S.91, D:T.93, D:E.98 CA.24: 4 residues within 4Å: Chain D: D.152, N.154, T.156, Q.158 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.152, D:T.156, D:Q.158, H2O.5, H2O.5

4 x GUN: GUANINE(Non-covalent)

GUN.6: 8 residues within 4Å: Chain A: N.154, G.155, T.156 Chain H: L.23, N.25, I.27, L.29, Q.49 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain H Hydrogen bonds: A:N.154, A:N.154, H:Q.49, H:Q.49 GUN.25: 4 residues within 4Å: Chain E: Y.22, S.57, T.58, V.60 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:S.57, E:S.57, E:T.58, E:T.58 pi-Stacking: E:Y.22, E:Y.22 pi-Cation interactions: E:Y.22 GUN.26: 11 residues within 4Å: Chain B: N.154, G.155, T.156 Chain E: L.23, I.27, L.29, Q.49 Chain F: Y.22, S.57, T.58, V.60 10 PLIP interactions: 2 interactions with chain B, 5 interactions with chain F, 3 interactions with chain E Hydrogen bonds: B:N.154, B:N.154, F:S.57, F:S.57, E:Q.49, E:Q.49 pi-Stacking: F:Y.22, F:Y.22 pi-Cation interactions: F:Y.22 Water bridges: E:N.25 GUN.27: 11 residues within 4Å: Chain D: N.154, G.155, T.156 Chain G: L.23, I.27, L.29, Q.49 Chain H: Y.22, S.57, T.58, V.60 11 PLIP interactions: 6 interactions with chain H, 3 interactions with chain G, 2 interactions with chain D Hydrogen bonds: H:S.57, H:S.57, H:T.58, G:Q.49, G:Q.49, D:N.154, D:N.154 pi-Stacking: H:Y.22, H:Y.22 pi-Cation interactions: H:Y.22 Water bridges: G:N.25

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

EDO.7: 5 residues within 4Å: Chain A: R.120, R.121 Chain B: A.54, D.57, G.62 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.57, B:G.62, A:R.120, A:R.121

2 x P4G: 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE(Non-covalent)

P4G.13: 4 residues within 4Å: Chain B: D.59 Chain D: S.58, E.67, Y.71 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:E.67 P4G.14: 4 residues within 4Å: Chain C: S.58, E.67, Y.71, R.146 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rizkallah, P.J. et al., Calpain small subunit 1, RNA-binding protein Hfq. Acta Crystallogr.,Sect.F (2020)

Release Date

2020-02-05

Peptides

Calpain small subunit 1: ABCD
RNA-binding protein Hfq: 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

Calpain small subunit 1

RNA-binding protein Hfq