SMTL ID : 8sgd.1 (1 other biounit)

Crystal Structure of CDC3(G) - CDC10(Delta 1-10) heterocomplex from Saccharomyces cerevisiae

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.66 Å

Oligo State

hetero-1-1-mer

Ligands

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

GDP.1: 17 residues within 4Å: Chain A: S.32, G.33, L.34, G.35, K.36, S.37, T.38, S.51, K.171, D.173, V.226, G.227, R.242 Chain B: T.156, H.158, I.186, E.191 20 PLIP interactions: 17 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.33, A:L.34, A:G.35, A:K.36, A:S.37, A:S.37, A:T.38, A:T.38, A:K.171, A:G.227, A:R.242, B:I.186 Water bridges: A:K.171, A:R.242, A:R.242, A:R.242 Salt bridges: A:K.36, A:D.173, B:H.158, B:H.158

6 x NA: SODIUM ION(Non-functional Binders)

NA.2: 1 residues within 4Å: Chain A: R.158 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.158 NA.3: 1 residues within 4Å: Chain A: K.107 No protein-ligand interaction detected (PLIP) NA.4: 3 residues within 4Å: Chain A: F.95, I.96 Chain B: P.162 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.96 NA.7: 2 residues within 4Å: Chain B: D.111, Q.112 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.112 NA.8: 3 residues within 4Å: Chain A: R.150 Chain B: H.76, L.108 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.150, B:H.76, B:L.108 NA.9: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.155

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.5: 17 residues within 4Å: Chain A: K.146, T.174, E.179 Chain B: D.24, G.25, I.26, G.27, K.28, T.29, T.30, K.183, D.185, I.239, G.240, R.256, Y.258 Ligands: MG.6 24 PLIP interactions: 18 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:G.25, B:I.26, B:G.27, B:K.28, B:T.29, B:T.30, B:T.30, B:K.183, B:G.240, B:R.256, B:R.256, B:Y.258, A:T.174 Water bridges: B:K.28, B:E.42, A:E.179, A:E.179, A:E.179, A:E.179 Salt bridges: B:K.28, B:K.28, B:D.185, A:K.146 pi-Cation interactions: B:R.256

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain B: T.29, E.42 Ligands: GTP.5 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.29, H2O.2, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marques da Silva, R. et al., A key piece of the puzzle: The central tetramer of the Saccharomyces cerevisiae septin protofilament and its implications for self-assembly. J.Struct.Biol. (2023)

Release Date

2023-06-28

Peptides

CDC10 isoform 1: A
CDC3 isoform 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

CDC10 isoform 1

CDC3 isoform 1

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