SMTL ID : 7m6j.1

Human Septin Hexameric Complex SEPT2G/SEPT6/SEPT7 by Single Particle Cryo-EM

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-mer

Ligands

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

GDP.1: 15 residues within 4Å: Chain A: S.13, G.14, L.15, G.16, K.17, S.18, T.19, K.150, D.152, V.207, G.208, R.223, Y.225 Chain B: A.188, E.193 14 PLIP interactions: 3 interactions with chain B, 11 interactions with chain A Hydrogen bonds: B:G.159, B:A.188, B:A.188, A:G.14, A:L.15, A:G.16, A:K.17, A:S.18, A:S.18, A:G.208, A:R.223 Salt bridges: A:K.17, A:D.152 pi-Cation interactions: A:R.223 GDP.3: 12 residues within 4Å: Chain C: G.55, L.56, G.57, K.58, S.59, T.60, S.79, K.190, G.245, R.260 Chain D: S.163, E.198 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.55, C:G.57, C:K.58, C:S.59, C:T.60, C:K.190, C:R.260, D:S.163 Salt bridges: C:K.58 GDP.4: 16 residues within 4Å: Chain C: T.193, E.198 Chain D: S.54, G.55, G.57, K.58, S.59, T.60, P.78, S.79, K.190, D.192, V.244, G.245, R.260, Y.262 15 PLIP interactions: 2 interactions with chain C, 13 interactions with chain D Hydrogen bonds: C:T.193, C:E.198, D:G.55, D:G.57, D:K.58, D:S.59, D:T.60, D:P.78, D:G.245, D:R.260, D:R.260, D:Y.262 Salt bridges: D:K.58, D:D.192 pi-Cation interactions: D:R.260 GDP.7: 18 residues within 4Å: Chain E: H.160, A.188, E.193 Chain F: E.12, S.13, G.14, L.15, G.16, K.17, S.18, T.19, R.33, K.150, D.152, V.207, G.208, R.223, Y.225 19 PLIP interactions: 15 interactions with chain F, 4 interactions with chain E Hydrogen bonds: F:S.13, F:G.14, F:L.15, F:G.16, F:K.17, F:S.18, F:T.19, F:G.208, F:R.223, F:R.223, F:Y.225, E:A.188, E:A.188 Salt bridges: F:K.17, F:R.33, F:R.33, F:D.152, E:H.160, E:H.160

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

GTP.2: 18 residues within 4Å: Chain A: H.125, T.153, E.158, R.161 Chain B: G.52, L.53, G.54, K.55, S.56, T.57, E.70, P.71, A.72, K.185, I.238, G.239, R.254, Y.256 22 PLIP interactions: 16 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:G.52, B:G.52, B:G.54, B:K.55, B:S.56, B:T.57, B:T.57, B:E.70, B:A.72, B:G.239, B:R.254, B:Y.256, A:T.153, A:E.158, A:R.161 Salt bridges: B:D.187, A:H.125, A:H.125, A:H.125 pi-Cation interactions: B:K.185, B:K.185, B:R.254 GTP.6: 19 residues within 4Å: Chain E: T.51, G.52, L.53, G.54, K.55, S.56, T.57, P.71, A.72, K.185, I.238, G.239, E.242, R.254 Chain F: H.125, T.153, E.158, R.161 Ligands: MG.5 19 PLIP interactions: 3 interactions with chain F, 16 interactions with chain E Hydrogen bonds: F:T.153, F:R.161, E:G.52, E:G.54, E:K.55, E:S.56, E:T.57, E:A.72, E:S.101, E:K.185, E:K.185, E:G.239, E:R.254, E:R.254 Salt bridges: F:H.125, E:K.55, E:K.55, E:D.187 pi-Cation interactions: E:R.254

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 2 residues within 4Å: Chain E: S.56 Ligands: GTP.6 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mendonca, D.C. et al., An atomic model for the human septin hexamer by cryo-EM. J.Mol.Biol. (2021)

Release Date

2021-07-07

Peptides

Septin-2: AF
Septin-6: BE
Septin-7: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
F

B
B

E
E

C
C

D
D

Septin-2

Septin-6

Septin-7

Related Entries With Identical Sequence