SMTL ID : 6hz7.1

Structure of McrBC without DNA binding domains (Class 3)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-12-2-mer

Ligands

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

GNP.1: 23 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 Chain B: E.137, D.139, K.140, A.184, R.187, R.188 Ligands: MG.2 21 PLIP interactions: 15 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:D.15, A:F.17, A:G.43, A:V.44, A:G.45, A:K.46, A:K.46, A:T.47, A:T.47, A:T.47, A:F.48, 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 pi-Stacking: A:F.17 GNP.3: 24 residues within 4Å: Chain B: 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 C: E.137, D.139, K.140, A.184, R.187, R.188 Ligands: MG.4 21 PLIP interactions: 15 interactions with chain B, 6 interactions with chain C Hydrogen bonds: 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:T.47, B:F.48, B:H.246, C:D.139, C:R.187, C:R.187, C:R.188, C:R.188 Salt bridges: B:D.15, C:K.140 pi-Stacking: B:F.17 pi-Cation interactions: B:F.206 GNP.5: 23 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, 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 24 PLIP interactions: 16 interactions with chain C, 8 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:K.46, C:T.47, C:T.47, C:T.47, C:F.48, C:S.247, D:D.139, 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 GNP.10: 23 residues within 4Å: Chain H: 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 Chain I: E.137, D.139, K.140, A.184, R.187, R.188 Ligands: MG.11 20 PLIP interactions: 5 interactions with chain I, 15 interactions with chain H Hydrogen bonds: I:R.187, I:R.187, I:R.188, I:R.188, H:D.15, H:F.17, H:G.43, H:V.44, H:G.45, H:K.46, H:K.46, H:T.47, H:T.47, H:T.47, H:F.48, H:H.246, H:S.247 Salt bridges: I:K.140, H:D.15 pi-Stacking: H:F.17 GNP.12: 24 residues within 4Å: Chain I: 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 J: E.137, D.139, K.140, A.184, R.187, R.188 Ligands: MG.13 22 PLIP interactions: 15 interactions with chain I, 7 interactions with chain J Hydrogen bonds: I:D.15, I:F.17, I:G.43, I:V.44, I:G.45, I:K.46, I:K.46, I:T.47, I:T.47, I:T.47, I:F.48, I:H.246, J:D.139, J:R.187, J:R.187, J:R.188, J:R.188 Salt bridges: I:D.15, J:K.140, J:R.187 pi-Stacking: I:F.17 pi-Cation interactions: I:F.206 GNP.14: 23 residues within 4Å: Chain J: D.15, L.16, F.17, P.41, P.42, G.43, V.44, G.45, K.46, T.47, F.48, N.172, H.246, S.247, C.250, C.251 Chain K: E.137, D.139, K.140, A.184, R.187, R.188 Ligands: MG.15 24 PLIP interactions: 16 interactions with chain J, 8 interactions with chain K Hydrogen bonds: J:D.15, J:F.17, J:G.43, J:V.44, J:G.45, J:K.46, J:K.46, J:T.47, J:T.47, J:T.47, J:F.48, J:S.247, K:D.139, K:D.139, K:R.187, K:R.187, K:R.188, K:R.188 Salt bridges: J:D.15, K:K.140, K:R.187 pi-Stacking: J:F.17, J:F.48, J:F.48

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.47, D.118 Chain B: R.188 Ligands: GNP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.47 MG.4: 6 residues within 4Å: Chain B: T.47, D.118 Chain C: K.140, R.187, R.188 Ligands: GNP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.47 MG.6: 5 residues within 4Å: Chain C: T.47 Chain D: K.140, R.187, R.188 Ligands: GNP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.47 MG.11: 5 residues within 4Å: Chain H: T.47, D.118 Chain I: K.140, R.188 Ligands: GNP.10 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:T.47 MG.13: 6 residues within 4Å: Chain I: T.47, D.118 Chain J: K.140, R.187, R.188 Ligands: GNP.12 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:T.47 MG.15: 4 residues within 4Å: Chain J: T.47 Chain K: R.187, R.188 Ligands: GNP.14 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:T.47

6 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 17 PLIP interactions: 16 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:F.48, 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 16 PLIP interactions: 13 interactions with chain E, 3 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:K.140, F:R.187 pi-Stacking: E:F.48 GDP.9: 17 residues within 4Å: Chain A: D.139, 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 16 PLIP interactions: 3 interactions with chain A, 13 interactions with chain F Salt bridges: A:K.140, A:K.140, A:R.187, F:K.46 Hydrogen bonds: F:D.15, F:D.15, F:F.17, F:G.43, F:V.44, F:G.45, F:K.46, F:T.47, F:T.47, F:S.247 pi-Stacking: F:F.48 pi-Cation interactions: F:F.17 GDP.16: 16 residues within 4Å: Chain K: 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 L: D.139, K.140 17 PLIP interactions: 16 interactions with chain K, 1 interactions with chain L Hydrogen bonds: K:D.15, K:D.15, K:F.17, K:G.43, K:V.44, K:G.45, K:K.46, K:T.47, K:T.47, K:F.48, K:H.246 Salt bridges: K:D.15, K:K.46, L:K.140 pi-Stacking: K:F.17, K:F.48 pi-Cation interactions: K:F.17 GDP.17: 19 residues within 4Å: Chain L: 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 M: E.137, D.139, K.140, R.187 17 PLIP interactions: 14 interactions with chain L, 3 interactions with chain M Hydrogen bonds: L:D.15, L:L.16, L:F.17, L:G.43, L:V.44, L:G.45, L:K.46, L:T.47, L:T.47, L:T.47, L:H.246, L:S.247 Salt bridges: L:K.46, M:K.140, M:K.140, M:R.187 pi-Stacking: L:F.48 GDP.18: 16 residues within 4Å: Chain H: K.140, R.187 Chain M: 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 17 PLIP interactions: 14 interactions with chain M, 3 interactions with chain H Hydrogen bonds: M:D.15, M:D.15, M:F.17, M:G.43, M:V.44, M:G.45, M:K.46, M:T.47, M:T.47, M:S.247 Salt bridges: M:K.46, H:K.140, H:K.140, H:R.187 pi-Stacking: M:F.48, M:F.48 pi-Cation interactions: M:F.17

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: ABCDEFHIJKLM
Protein McrC: GN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

H
G

I
H

J
I

K
J

L
K

M
L

G
M

N
N

5-methylcytosine-specific restriction enzyme B

Protein McrC

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