SMTL ID : 9gd4.1

Crystal structure of septin complex Shs1-Cdc12-Cdc3-Cdc10 from Saccharomyces cerevisiae

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

4 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 20 residues within 4Å: Chain A: Q.18, S.19, G.20, L.21, G.22, K.23, S.24, T.25, S.38, K.158, D.160, V.213, G.214, R.229 Chain B: T.182, G.183, H.184, I.212, L.213, E.217 28 PLIP interactions: 22 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:Q.18, A:G.20, A:L.21, A:G.22, A:K.23, A:S.24, A:S.24, A:T.25, A:S.38, A:K.158, A:G.214, A:R.229, B:I.212, B:E.217, B:E.217 Water bridges: A:K.23, A:T.25, A:A.39, A:T.40, A:T.40, A:K.158, A:R.229, A:R.229, A:R.229 Salt bridges: A:D.160, B:H.184, B:H.184, B:E.217 GDP.2: 22 residues within 4Å: Chain A: N.131, G.132, K.133, T.161, L.162, E.166 Chain B: P.49, D.50, G.51, I.52, G.53, K.54, T.55, T.56, K.209, D.211, I.212, I.265, G.266, R.282, Y.284 Ligands: MG.3 25 PLIP interactions: 19 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:P.49, B:G.51, B:I.52, B:G.53, B:K.54, B:T.55, B:T.56, B:T.56, B:G.266, B:R.282, A:T.161, A:E.166, A:E.166 Water bridges: B:D.50, B:K.54, B:T.55, B:K.209, B:K.209, B:K.209 Salt bridges: B:K.54, B:D.211, A:K.133, A:K.133, A:E.166 pi-Cation interactions: B:R.282 GDP.5: 20 residues within 4Å: Chain C: S.59, G.60, L.61, G.62, K.63, T.64, T.65, K.196, D.198, T.199, V.262, G.263, R.279, Y.281 Chain D: T.172, G.173, H.174, S.202, F.203, E.207 27 PLIP interactions: 18 interactions with chain C, 9 interactions with chain D Hydrogen bonds: C:G.60, C:L.61, C:G.62, C:K.63, C:T.64, C:T.64, C:T.65, C:K.196, C:G.263, C:R.279, D:S.202, D:E.207 Water bridges: C:K.63, C:K.63, C:T.64, C:K.196, C:K.266, D:G.173, D:G.173, D:H.174, D:H.174 Salt bridges: C:K.63, C:D.198, D:H.174, D:H.174, D:E.207 pi-Cation interactions: C:R.279 GDP.6: 23 residues within 4Å: Chain C: T.169, G.170, H.171, T.199, L.200, E.204 Chain D: P.12, A.13, G.14, T.15, G.16, K.17, T.18, A.19, H.32, K.33, R.199, D.201, S.202, I.256, T.257, R.269, Y.271 25 PLIP interactions: 5 interactions with chain C, 20 interactions with chain D Hydrogen bonds: C:T.199, C:E.204, C:E.204, D:P.12, D:G.14, D:T.15, D:G.16, D:K.17, D:T.18, D:T.18, D:A.19, D:R.199, D:R.199, D:R.199, D:T.257, D:T.257, D:R.269 Salt bridges: C:H.171, C:H.171, D:K.17, D:H.32, D:D.201 Water bridges: D:K.17, D:T.18 pi-Cation interactions: D:R.269

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain B: T.55 Ligands: GDP.2 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.55, H2O.6, H2O.6, H2O.7

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

SO4.4: 5 residues within 4Å: Chain A: R.137 Chain B: H.102, F.133, L.134, N.135 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.134, B:N.135 Salt bridges: B:H.102, A:R.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grupp, B. et al., Crystal structure of septin complex Shs1-Cdc12-Cdc3-Cdc10 from Saccharomyces cerevisiae. To Be Published

Release Date

2025-02-05

Peptides

Cell division control protein 10: A
Cell division control protein 3: B
Cell division control protein 12: C
Seventh homolog of septin 1: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Cell division control protein 10

Cell division control protein 3

Cell division control protein 12

Seventh homolog of septin 1

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