SMTL ID : 4ds7.6 (5 other biounits)

Crystal structure of yeast calmodulin bound to the C-terminal fragment of spindle pole body protein Spc110

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-4-4-mer

Ligands

8 x SR: STRONTIUM ION(Non-functional Binders)

SR.1: 5 residues within 4Å: Chain A: D.21, D.23, S.25, S.27, E.32 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.23, A:S.25, A:E.32, A:E.32, H2O.2 SR.2: 5 residues within 4Å: Chain A: D.94, N.96, D.98, L.100, E.105 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.94, A:D.98, A:L.100, A:E.105, H2O.2 SR.5: 5 residues within 4Å: Chain B: D.21, D.23, S.25, S.27, E.32 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.25, B:E.32, B:E.32, H2O.4, H2O.4 SR.6: 5 residues within 4Å: Chain B: D.94, N.96, D.98, L.100, E.105 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.94, B:D.98, B:L.100, B:E.105, H2O.4 SR.10: 5 residues within 4Å: Chain E: D.21, D.23, S.25, S.27, E.32 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.23, E:S.25, E:E.32, E:E.32, H2O.7 SR.11: 5 residues within 4Å: Chain E: D.94, N.96, D.98, L.100, E.105 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.94, E:D.98, E:L.100, E:E.105, H2O.7 SR.14: 5 residues within 4Å: Chain F: D.21, D.23, S.25, S.27, E.32 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:S.25, F:E.32, F:E.32, H2O.9, H2O.9 SR.15: 5 residues within 4Å: Chain F: D.94, N.96, D.98, L.100, E.105 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.94, F:D.98, F:L.100, F:E.105, H2O.9

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.7: 4 residues within 4Å: Chain B: K.107, L.117, T.118, D.119 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.107, B:D.119, B:D.119 Water bridges: B:T.118, B:A.120 GOL.8: 3 residues within 4Å: Chain B: G.114, E.115, K.116 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.114, B:K.116 GOL.9: 7 residues within 4Å: Chain A: S.39, L.40, G.41 Chain B: V.92, H.108, V.109, S.112 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.92, B:S.112, B:S.112 GOL.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.16: 4 residues within 4Å: Chain F: K.107, L.117, T.118, D.119 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:K.107, F:D.119, F:D.119 Water bridges: F:T.118, F:A.120 GOL.17: 3 residues within 4Å: Chain F: G.114, E.115, K.116 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:G.114, F:K.116 GOL.18: 7 residues within 4Å: Chain E: S.39, L.40, G.41 Chain F: V.92, H.108, V.109, S.112 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:V.92, F:S.112, F:S.112

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

SO4.4: 2 residues within 4Å: Chain A: T.118, D.119 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.119, A:D.119 Water bridges: A:A.120 SO4.13: 2 residues within 4Å: Chain E: T.118, D.119 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:D.119, E:D.119 Water bridges: E:A.120

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Viswanath, S. et al., The molecular architecture of the yeast spindle pole body core determined by Bayesian integrative modeling. Mol.Biol.Cell (2017)

Release Date

2012-03-07

Peptides

Calmodulin: ABEF
Spindle pole body component 110: CDGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
A

F
B

C
E

D
F

G
E

H
F

Calmodulin

Spindle pole body component 110

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