SMTL ID : 6ut3.1

X-ray structure of Thermococcus gammatolerans McrB AAA+ domain hexamer in P21 symmetry

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

homo-hexamer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain B: T.37, D.171, E.172 Chain C: R.241 Ligands: GSP.2 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.37 MG.4: 5 residues within 4Å: Chain C: T.37, D.171, E.172 Chain D: R.241 Ligands: GSP.3 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.37 MG.6: 5 residues within 4Å: Chain D: T.37, D.171, E.172 Chain E: R.241 Ligands: GSP.5 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:T.37, D:D.171, D:E.172 MG.8: 5 residues within 4Å: Chain E: T.37, D.171, E.172, T.223 Ligands: GSP.7 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:T.37, E:D.171

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

GSP.2: 20 residues within 4Å: Chain B: P.32, G.33, T.34, G.35, K.36, T.37, W.38, E.172, I.262, H.316, S.317, L.320 Chain C: E.190, D.192, K.193, N.199, A.237, R.240, R.241 Ligands: MG.1 23 PLIP interactions: 10 interactions with chain C, 13 interactions with chain B Hydrogen bonds: C:D.192, C:K.193, C:K.193, C:N.199, C:R.240, C:R.241, C:R.241, B:G.35, B:K.36, B:K.36, B:K.36, B:T.37, B:W.38, B:K.265, B:K.265, B:S.317 Salt bridges: C:K.193, C:R.240, C:R.240, B:K.36 pi-Stacking: B:W.38, B:W.38 pi-Cation interactions: B:W.38 GSP.3: 21 residues within 4Å: Chain C: P.31, P.32, G.33, T.34, G.35, K.36, T.37, W.38, E.172, F.253, H.316, S.317, L.320 Chain D: E.190, D.192, K.193, N.199, A.237, R.240, R.241 Ligands: MG.4 19 PLIP interactions: 8 interactions with chain D, 11 interactions with chain C Hydrogen bonds: D:D.192, D:D.192, D:N.199, D:R.241, C:P.31, C:G.33, C:K.36, C:K.36, C:T.37, C:T.37, C:W.38 Salt bridges: D:K.193, D:K.193, D:R.240, D:R.240, C:K.36 pi-Stacking: C:W.38, C:W.38 pi-Cation interactions: C:W.38 GSP.5: 19 residues within 4Å: Chain D: P.32, G.33, T.34, G.35, K.36, T.37, W.38, E.172, H.316, S.317, L.320 Chain E: E.190, D.192, K.193, N.199, A.237, R.240, R.241 Ligands: MG.6 19 PLIP interactions: 8 interactions with chain E, 11 interactions with chain D Hydrogen bonds: E:K.193, E:N.199, E:R.240, E:R.241, E:R.241, D:G.33, D:T.34, D:K.36, D:T.37, D:T.37, D:W.38 Salt bridges: E:K.193, E:R.240, E:R.240, D:K.36 pi-Stacking: D:W.38, D:W.38 pi-Cation interactions: D:W.38, D:W.38 GSP.7: 19 residues within 4Å: Chain E: P.32, T.34, G.35, K.36, T.37, W.38, E.172, T.223, I.262, H.316, S.317, L.320 Chain F: E.190, D.192, K.193, N.199, R.240, R.241 Ligands: MG.8 21 PLIP interactions: 9 interactions with chain F, 12 interactions with chain E Hydrogen bonds: F:D.192, F:D.192, F:N.199, F:R.240, F:R.241, F:R.241, E:P.32, E:K.36, E:T.37, E:T.37, E:W.38 Salt bridges: F:K.193, F:R.240, F:R.240, E:K.36, E:K.36 pi-Stacking: E:W.38, E:W.38, E:W.38 pi-Cation interactions: E:W.38, 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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

GTPase subunit of restriction endonuclease

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