SMTL ID : 6hz4.1

Structure of McrBC without DNA binding domains (one half of the full complex)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-2-mer

Ligands

3 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)

GNP.1: 24 residues within 4Å: Chain A: D.15, L.16, F.17, P.42, G.43, V.44, G.45, K.46, T.47, F.48, E.119, N.172, F.206, H.246, S.247, C.250, C.251 Chain B: E.137, D.139, K.140, A.184, R.187, R.188 Ligands: MG.2 19 PLIP interactions: 13 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:D.15, A:F.17, A:G.43, A:G.45, A:K.46, A:K.46, A:T.47, A:T.47, A:F.48, A:E.119, A:H.246, A:S.247, B:R.187, B:R.187, B:R.188, B:R.188 Salt bridges: A:D.15, B:K.140, B:R.187 GNP.3: 24 residues within 4Å: Chain B: D.15, L.16, F.17, P.41, P.42, G.43, V.44, G.45, K.46, T.47, F.48, E.119, N.172, H.246, S.247, C.250, C.251 Chain C: E.137, D.139, K.140, A.184, R.187, R.188 Ligands: MG.4 25 PLIP interactions: 8 interactions with chain C, 17 interactions with chain B Hydrogen bonds: C:D.139, C:A.184, C:R.187, C:R.187, C:R.188, C:R.188, B:D.15, B:F.17, B:G.43, B:V.44, B:G.45, B:K.46, B:K.46, B:T.47, B:T.47, B:F.48, B:E.119, B:H.246 Salt bridges: C:K.140, C:R.187, B:D.15 pi-Stacking: B:F.17, B:F.17, B:F.48 pi-Cation interactions: B:F.206 GNP.5: 24 residues within 4Å: Chain C: D.15, L.16, F.17, P.41, P.42, G.43, V.44, G.45, K.46, T.47, F.48, N.172, F.206, H.246, S.247, C.250, C.251 Chain D: E.137, D.139, K.140, A.184, R.187, R.188 Ligands: MG.6 21 PLIP interactions: 14 interactions with chain C, 7 interactions with chain D Hydrogen bonds: C:D.15, C:F.17, C:G.43, C:V.44, C:G.45, C:K.46, C:T.47, C:T.47, C:F.48, C:S.247, D:D.139, D:R.187, D:R.187, D:R.188, D:R.188 Salt bridges: C:D.15, D:K.140, D:R.187 pi-Stacking: C:F.17, C:F.48, C:F.48

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: T.47, D.118 Chain B: K.140, R.188 Ligands: GNP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.47, A:D.118 MG.4: 4 residues within 4Å: Chain B: T.47, D.118 Chain C: R.188 Ligands: GNP.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.47, B:D.118 MG.6: 4 residues within 4Å: Chain C: T.47, D.118 Chain D: R.188 Ligands: GNP.5 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.47, C:D.118

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

GDP.7: 16 residues within 4Å: Chain D: D.15, L.16, F.17, P.42, G.43, V.44, G.45, K.46, T.47, F.48, H.246, S.247, C.250, C.251 Chain E: D.139, K.140 16 PLIP interactions: 15 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:D.15, D:D.15, D:F.17, D:G.43, D:V.44, D:G.45, D:K.46, D:T.47, D:T.47, D:H.246 Salt bridges: D:D.15, D:K.46, E:K.140 pi-Stacking: D:F.17, D:F.48 pi-Cation interactions: D:F.17 GDP.8: 19 residues within 4Å: Chain E: D.15, L.16, F.17, P.42, G.43, V.44, G.45, K.46, T.47, F.48, F.206, H.246, S.247, C.250, C.251 Chain F: E.137, D.139, K.140, R.187 17 PLIP interactions: 15 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:D.15, E:F.17, E:G.43, E:V.44, E:G.45, E:K.46, E:T.47, E:T.47, E:T.47, E:H.246, E:S.247 Salt bridges: E:K.46, F:K.140, F:R.187 pi-Stacking: E:F.48, E:F.48 pi-Cation interactions: E:F.48 GDP.9: 16 residues within 4Å: Chain A: K.140, R.187 Chain F: D.15, L.16, F.17, P.42, G.43, V.44, G.45, K.46, T.47, F.48, H.246, S.247, C.250, C.251 15 PLIP interactions: 12 interactions with chain F, 3 interactions with chain A Hydrogen bonds: F:D.15, F:F.17, F:G.43, F:G.45, F:K.46, F:T.47, F:T.47, F:S.247 Salt bridges: F:K.46, A:K.140, A:K.140, A:R.187 pi-Stacking: F:F.48, F:F.48 pi-Cation interactions: F:F.48

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nirwan, N. et al., Structure-based mechanism for activation of the AAA+ GTPase McrB by the endonuclease McrC. Nat Commun (2019)

Release Date

2019-07-24

Peptides

5-methylcytosine-specific restriction enzyme B: ABCDEF
Protein McrC: GH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
M

H
N

5-methylcytosine-specific restriction enzyme B

Protein McrC

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