SMTL ID : 5jyg.1

Cryo-EM structure of the MamK filament at 6.5 A

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-14-mer

Ligands

14 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: E.143, D.161 Ligands: ADP.2 No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain B: E.143, D.161 Ligands: ADP.4 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain C: E.143 Ligands: ADP.6 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain D: L.18, E.143, D.161 Ligands: ADP.8 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain E: E.143, D.161 Ligands: ADP.10 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain F: E.143, D.161 Ligands: ADP.12 No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Chain G: E.143 Ligands: ADP.14 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Chain H: E.143 Ligands: ADP.16 No protein-ligand interaction detected (PLIP) MG.17: 4 residues within 4Å: Chain I: L.18, E.143, D.161 Ligands: ADP.18 No protein-ligand interaction detected (PLIP) MG.19: 3 residues within 4Å: Chain J: E.143, D.161 Ligands: ADP.20 No protein-ligand interaction detected (PLIP) MG.21: 3 residues within 4Å: Chain K: E.143, D.161 Ligands: ADP.22 No protein-ligand interaction detected (PLIP) MG.23: 2 residues within 4Å: Chain L: E.143 Ligands: ADP.24 No protein-ligand interaction detected (PLIP) MG.25: 4 residues within 4Å: Chain M: L.18, E.143, D.161 Ligands: ADP.26 No protein-ligand interaction detected (PLIP) MG.27: 3 residues within 4Å: Chain N: E.143, D.161 Ligands: ADP.28 No protein-ligand interaction detected (PLIP)

14 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 13 residues within 4Å: Chain A: G.19, T.20, S.21, G.163, A.164, G.165, C.215, K.218, E.219, S.222, G.289, R.292 Ligands: MG.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:T.20, A:S.21, A:A.164, A:G.165, A:K.218, A:S.222, A:G.289, A:R.292, A:R.292 ADP.4: 15 residues within 4Å: Chain B: G.19, T.20, S.21, H.22, I.162, G.163, A.164, K.218, E.219, S.222, G.288, G.289, R.292, I.293 Ligands: MG.3 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.20, B:S.21, B:H.22, B:A.164, B:S.222, B:G.289, B:R.292 ADP.6: 15 residues within 4Å: Chain C: G.19, T.20, S.21, H.22, G.163, A.164, G.165, K.218, E.219, S.222, G.288, G.289, R.292, I.293 Ligands: MG.5 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:T.20, C:S.21, C:A.164, C:G.165, C:K.218, C:E.219, C:S.222, C:G.289, C:R.292 Salt bridges: C:H.22 ADP.8: 14 residues within 4Å: Chain D: G.19, T.20, S.21, D.76, G.163, A.164, G.165, C.215, K.218, E.219, S.222, G.289, R.292 Ligands: MG.7 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:T.20, D:T.20, D:S.21, D:D.76, D:A.164, D:G.165, D:K.218, D:E.219, D:S.222, D:G.289, D:R.292, D:R.292 ADP.10: 13 residues within 4Å: Chain E: G.19, T.20, S.21, G.163, A.164, G.165, C.215, K.218, E.219, S.222, G.289, R.292 Ligands: MG.9 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:T.20, E:S.21, E:A.164, E:G.165, E:K.218, E:S.222, E:G.289, E:R.292, E:R.292 ADP.12: 15 residues within 4Å: Chain F: G.19, T.20, S.21, H.22, I.162, G.163, A.164, K.218, E.219, S.222, G.288, G.289, R.292, I.293 Ligands: MG.11 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:T.20, F:S.21, F:H.22, F:A.164, F:S.222, F:G.289, F:R.292 ADP.14: 15 residues within 4Å: Chain G: G.19, T.20, S.21, H.22, G.163, A.164, G.165, K.218, E.219, S.222, G.288, G.289, R.292, I.293 Ligands: MG.13 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:T.20, G:S.21, G:A.164, G:G.165, G:K.218, G:E.219, G:S.222, G:G.289, G:R.292 Salt bridges: G:H.22 ADP.16: 15 residues within 4Å: Chain H: G.19, T.20, S.21, H.22, G.163, A.164, G.165, K.218, E.219, S.222, G.288, G.289, R.292, I.293 Ligands: MG.15 10 PLIP interactions: 10 interactions with chain H Hydrogen bonds: H:T.20, H:S.21, H:A.164, H:G.165, H:K.218, H:E.219, H:S.222, H:G.289, H:R.292 Salt bridges: H:H.22 ADP.18: 14 residues within 4Å: Chain I: G.19, T.20, S.21, D.76, G.163, A.164, G.165, C.215, K.218, E.219, S.222, G.289, R.292 Ligands: MG.17 14 PLIP interactions: 14 interactions with chain I Hydrogen bonds: I:T.20, I:T.20, I:S.21, I:D.76, I:D.76, I:D.76, I:A.164, I:G.165, I:K.218, I:E.219, I:S.222, I:G.289, I:R.292, I:R.292 ADP.20: 13 residues within 4Å: Chain J: G.19, T.20, S.21, G.163, A.164, G.165, C.215, K.218, E.219, S.222, G.289, R.292 Ligands: MG.19 9 PLIP interactions: 9 interactions with chain J Hydrogen bonds: J:T.20, J:S.21, J:A.164, J:G.165, J:K.218, J:S.222, J:G.289, J:R.292, J:R.292 ADP.22: 15 residues within 4Å: Chain K: G.19, T.20, S.21, H.22, I.162, G.163, A.164, K.218, E.219, S.222, G.288, G.289, R.292, I.293 Ligands: MG.21 7 PLIP interactions: 7 interactions with chain K Hydrogen bonds: K:T.20, K:S.21, K:H.22, K:A.164, K:S.222, K:G.289, K:R.292 ADP.24: 15 residues within 4Å: Chain L: G.19, T.20, S.21, H.22, G.163, A.164, G.165, K.218, E.219, S.222, G.288, G.289, R.292, I.293 Ligands: MG.23 10 PLIP interactions: 10 interactions with chain L Hydrogen bonds: L:T.20, L:S.21, L:A.164, L:G.165, L:K.218, L:E.219, L:S.222, L:G.289, L:R.292 Salt bridges: L:H.22 ADP.26: 13 residues within 4Å: Chain M: G.19, T.20, S.21, G.163, A.164, G.165, C.215, K.218, E.219, S.222, G.289, R.292 Ligands: MG.25 11 PLIP interactions: 11 interactions with chain M Hydrogen bonds: M:T.20, M:T.20, M:S.21, M:A.164, M:G.165, M:K.218, M:E.219, M:S.222, M:G.289, M:R.292, M:R.292 ADP.28: 13 residues within 4Å: Chain N: G.19, T.20, S.21, G.163, A.164, G.165, C.215, K.218, E.219, S.222, G.289, R.292 Ligands: MG.27 9 PLIP interactions: 9 interactions with chain N Hydrogen bonds: N:T.20, N:S.21, N:A.164, N:G.165, N:K.218, N:S.222, N:G.289, N:R.292, N:R.292

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bergeron, J.R. et al., Structure of the magnetosome-associated actin-like MamK filament at subnanometer resolution. Protein Sci. (2017)

Release Date

2016-07-27

Peptides

Actin-like ATPase: ABCDEFGHIJKLMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

Actin-like ATPase