SMTL ID : 6ut8.1

Refined half-complex from tetradecameric assembly of Thermococcus gammatolerans McrB AAA+ hexamers with bound McrC

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

2 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: 10 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.33, A:G.35, A:T.37, A:T.37, A:W.38 Salt bridges: A:K.36, B:R.240 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

6 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

4 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: 23 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.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: 11 interactions with chain C, 9 interactions with chain D Hydrogen bonds: C:G.33, C:K.36, C:K.36, C:T.37, C:W.38, C:K.265, C:K.266, D:D.192, D:N.199, D:R.240, D:R.241, D:R.241 Salt bridges: C:K.36, D:K.193, D:R.240, D:R.240, D:R.241 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: 8 interactions with chain E, 10 interactions with chain D Hydrogen bonds: E:D.192, E:N.199, E:A.237, E:R.241, D:K.36, D:T.37, D:T.37, D:W.38, D:W.38, D:K.265, D:K.265 Salt bridges: E:K.193, E:R.240, E:R.240, E:R.241 pi-Stacking: D:W.38, D:W.38 pi-Cation interactions: D:W.38 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: 10 interactions with chain F, 12 interactions with chain E Hydrogen bonds: F:D.192, F:N.199, F:V.236, F:R.241, F:R.241, E:G.33, E:K.36, E:K.36, E:K.36, E:T.37, E:T.37, E:W.38, E:E.172 Salt bridges: F:K.193, F:K.193, F:R.240, F:R.240, F:R.241, E:K.36 pi-Stacking: E:W.38, E:W.38 pi-Cation interactions: E: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: ABCDEF
McrBC 5-methylcytosine restriction system component: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

GTPase subunit of restriction endonuclease

McrBC 5-methylcytosine restriction system component

Related Entries With Identical Sequence