SMTL ID : 6ut7.1

Fitted model for the tetradecameric assembly of Thermococcus gammatolerans McrB AAA+ hexamers with bound McrC

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-12-2-mer

Ligands

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

GDP.1: 14 residues within 4Å: Chain A: P.32, G.33, T.34, G.35, K.36, T.37, W.38, F.253, I.262, H.316, S.317, L.320 Chain B: R.240 Ligands: MG.2 11 PLIP interactions: 1 interactions with chain B, 10 interactions with chain A Salt bridges: B:R.240, A:K.36 Hydrogen bonds: A:G.33, A:G.35, A:T.37, A:T.37, A:W.38 pi-Stacking: A:W.38, A:W.38, A:W.38 pi-Cation interactions: A:W.38 GDP.11: 15 residues within 4Å: Chain A: E.190 Chain F: I.9, P.32, G.33, T.34, G.35, K.36, T.37, W.38, N.225, I.262, K.266, S.317, L.320 Ligands: MG.12 17 PLIP interactions: 16 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:G.33, F:T.34, F:G.35, F:K.36, F:T.37, F:T.37, F:W.38, F:N.225, F:K.266, F:K.266, F:S.317, A:D.192 Salt bridges: F:K.36 pi-Stacking: F:W.38, F:W.38, F:W.38 pi-Cation interactions: F:W.38 GDP.13: 14 residues within 4Å: Chain H: P.32, G.33, T.34, G.35, K.36, T.37, W.38, F.253, I.262, H.316, S.317, L.320 Chain I: R.240 Ligands: MG.14 11 PLIP interactions: 10 interactions with chain H, 1 interactions with chain I Hydrogen bonds: H:G.33, H:G.35, H:T.37, H:T.37, H:W.38 Salt bridges: H:K.36, I:R.240 pi-Stacking: H:W.38, H:W.38, H:W.38 pi-Cation interactions: H:W.38 GDP.23: 15 residues within 4Å: Chain H: E.190 Chain M: I.9, P.32, G.33, T.34, G.35, K.36, T.37, W.38, N.225, I.262, K.266, S.317, L.320 Ligands: MG.24 17 PLIP interactions: 16 interactions with chain M, 1 interactions with chain H Hydrogen bonds: M:G.33, M:T.34, M:G.35, M:K.36, M:T.37, M:T.37, M:W.38, M:N.225, M:K.266, M:K.266, M:S.317, H:D.192 Salt bridges: M:K.36 pi-Stacking: M:W.38, M:W.38, M:W.38 pi-Cation interactions: M:W.38

12 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.37, D.171, T.223 Ligands: GDP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.37, A:D.171 MG.4: 3 residues within 4Å: Chain B: T.37, D.171 Ligands: GSP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.37 MG.6: 4 residues within 4Å: Chain C: T.37, D.171 Chain D: R.241 Ligands: GSP.5 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.37, C:D.171 MG.8: 7 residues within 4Å: Chain D: T.37, D.171, E.172, T.223 Chain E: T.187, R.241 Ligands: GSP.7 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:T.37, D:D.171, D:D.171 MG.10: 5 residues within 4Å: Chain E: T.37, D.171, E.172 Chain F: R.241 Ligands: GSP.9 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:T.37, E:D.171 MG.12: 3 residues within 4Å: Chain F: T.37, D.171 Ligands: GDP.11 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.37 MG.14: 4 residues within 4Å: Chain H: T.37, D.171, T.223 Ligands: GDP.13 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:T.37, H:D.171 MG.16: 3 residues within 4Å: Chain I: T.37, D.171 Ligands: GSP.15 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:T.37 MG.18: 4 residues within 4Å: Chain J: T.37, D.171 Chain K: R.241 Ligands: GSP.17 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:T.37, J:D.171 MG.20: 7 residues within 4Å: Chain K: T.37, D.171, E.172, T.223 Chain L: T.187, R.241 Ligands: GSP.19 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:T.37, K:D.171, K:D.171 MG.22: 5 residues within 4Å: Chain L: T.37, D.171, E.172 Chain M: R.241 Ligands: GSP.21 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:T.37, L:D.171 MG.24: 3 residues within 4Å: Chain M: T.37, D.171 Ligands: GDP.23 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:T.37

8 x GSP: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE(Non-covalent)

GSP.3: 22 residues within 4Å: Chain B: P.32, T.34, G.35, K.36, T.37, W.38, E.172, N.225, F.253, I.262, K.265, H.316, S.317, L.320 Chain C: E.190, D.192, K.193, N.199, A.237, R.240, R.241 Ligands: MG.4 22 PLIP interactions: 13 interactions with chain B, 9 interactions with chain C Hydrogen bonds: B:K.36, B:K.36, B:K.36, B:T.37, B:T.37, B:W.38, B:E.172, B:K.265, B:K.265, C:D.192, C:N.199, C:R.241, C:R.241 Salt bridges: B:K.36, C:K.193, C:K.193, C:R.240, C:R.240, C:R.241 pi-Stacking: B:W.38, B:W.38 pi-Cation interactions: B:W.38 GSP.5: 24 residues within 4Å: Chain C: P.32, T.34, G.35, K.36, T.37, W.38, D.171, E.172, N.225, F.253, I.262, K.265, K.266, H.316, S.317, L.320 Chain D: E.190, D.192, K.193, N.199, A.237, R.240, R.241 Ligands: MG.6 20 PLIP interactions: 9 interactions with chain D, 11 interactions with chain C Hydrogen bonds: D:D.192, D:N.199, D:R.240, D:R.241, D:R.241, C:G.33, C:K.36, C:K.36, C:T.37, C:W.38, C:K.265, C:K.266 Salt bridges: D:K.193, D:R.240, D:R.240, D:R.241, C:K.36 pi-Stacking: C:W.38, C:W.38 pi-Cation interactions: C:W.38 GSP.7: 22 residues within 4Å: Chain D: P.32, T.34, G.35, K.36, T.37, W.38, E.172, N.225, F.253, I.262, K.265, H.316, S.317, L.320 Chain E: E.190, D.192, K.193, N.199, A.237, R.240, R.241 Ligands: MG.8 18 PLIP interactions: 10 interactions with chain D, 8 interactions with chain E Hydrogen bonds: D:K.36, D:T.37, D:T.37, D:W.38, D:W.38, D:K.265, D:K.265, E:D.192, E:N.199, E:A.237, E:R.241 pi-Stacking: D:W.38, D:W.38 pi-Cation interactions: D:W.38 Salt bridges: E:K.193, E:R.240, E:R.240, E:R.241 GSP.9: 22 residues within 4Å: Chain E: P.32, G.33, T.34, G.35, K.36, T.37, W.38, E.172, N.225, F.253, I.262, H.316, S.317, L.320 Chain F: E.190, D.192, K.193, N.199, V.236, R.240, R.241 Ligands: MG.10 22 PLIP interactions: 12 interactions with chain E, 10 interactions with chain F Hydrogen bonds: E:G.33, E:K.36, E:K.36, E:K.36, E:T.37, E:T.37, E:W.38, E:E.172, F:D.192, F:N.199, F:V.236, F:R.241, F:R.241 Salt bridges: E:K.36, F:K.193, F:K.193, F:R.240, F:R.240, F:R.241 pi-Stacking: E:W.38, E:W.38 pi-Cation interactions: E:W.38 GSP.15: 22 residues within 4Å: Chain I: P.32, T.34, G.35, K.36, T.37, W.38, E.172, N.225, F.253, I.262, K.265, H.316, S.317, L.320 Chain J: E.190, D.192, K.193, N.199, A.237, R.240, R.241 Ligands: MG.16 23 PLIP interactions: 9 interactions with chain J, 14 interactions with chain I Hydrogen bonds: J:D.192, J:N.199, J:R.241, J:R.241, I:K.36, I:K.36, I:K.36, I:T.37, I:T.37, I:T.37, I:W.38, I:E.172, I:K.265, I:K.265 Salt bridges: J:K.193, J:K.193, J:R.240, J:R.240, J:R.241, I:K.36 pi-Stacking: I:W.38, I:W.38 pi-Cation interactions: I:W.38 GSP.17: 23 residues within 4Å: Chain J: P.32, T.34, G.35, K.36, T.37, W.38, D.171, E.172, N.225, F.253, I.262, K.266, H.316, S.317, L.320 Chain K: E.190, D.192, K.193, N.199, A.237, R.240, R.241 Ligands: MG.18 20 PLIP interactions: 11 interactions with chain J, 9 interactions with chain K Hydrogen bonds: J:G.33, J:K.36, J:K.36, J:T.37, J:W.38, J:K.265, J:K.266, K:D.192, K:N.199, K:R.240, K:R.241, K:R.241 Salt bridges: J:K.36, K:K.193, K:R.240, K:R.240, K:R.241 pi-Stacking: J:W.38, J:W.38 pi-Cation interactions: J:W.38 GSP.19: 22 residues within 4Å: Chain K: P.32, T.34, G.35, K.36, T.37, W.38, E.172, N.225, F.253, I.262, K.265, H.316, S.317, L.320 Chain L: E.190, D.192, K.193, N.199, A.237, R.240, R.241 Ligands: MG.20 18 PLIP interactions: 10 interactions with chain K, 8 interactions with chain L Hydrogen bonds: K:K.36, K:T.37, K:T.37, K:W.38, K:W.38, K:K.265, K:K.265, L:D.192, L:N.199, L:A.237, L:R.241 pi-Stacking: K:W.38, K:W.38 pi-Cation interactions: K:W.38 Salt bridges: L:K.193, L:R.240, L:R.240, L:R.241 GSP.21: 22 residues within 4Å: Chain L: P.32, G.33, T.34, G.35, K.36, T.37, W.38, E.172, N.225, F.253, I.262, H.316, S.317, L.320 Chain M: E.190, D.192, K.193, N.199, V.236, R.240, R.241 Ligands: MG.22 22 PLIP interactions: 10 interactions with chain M, 12 interactions with chain L Hydrogen bonds: M:D.192, M:N.199, M:V.236, M:R.241, M:R.241, L:G.33, L:K.36, L:K.36, L:K.36, L:T.37, L:T.37, L:W.38, L:E.172 Salt bridges: M:K.193, M:K.193, M:R.240, M:R.240, M:R.241, L:K.36 pi-Stacking: L:W.38, L:W.38 pi-Cation interactions: L:W.38

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Niu, Y. et al., Structural asymmetry governs the assembly and GTPase activity of McrBC restriction complexes. Nat Commun (2020)

Release Date

2020-10-21

Peptides

GTPase subunit of restriction endonuclease: ABCDEFHIJKLM
McrBC 5-methylcytosine restriction system component: GN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

H
H

I
I

J
J

K
K

L
L

M
M

G
G

N
N

GTPase subunit of restriction endonuclease

McrBC 5-methylcytosine restriction system component

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