SMTL ID : 7vsr.1

Structure of McrBC (stalkless mutant)

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: 24 residues within 4Å: Chain A: D.176, L.177, F.178, P.202, P.203, G.204, V.205, G.206, K.207, T.208, F.209, E.280, N.333, H.407, S.408, C.411, C.412 Chain B: E.298, D.300, K.301, A.345, R.348, R.349 Ligands: MG.2 22 PLIP interactions: 15 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:D.176, A:F.178, A:P.202, A:G.204, A:V.205, A:G.206, A:K.207, A:K.207, A:T.208, A:T.208, A:F.209, A:E.280, A:H.407, B:E.298, B:R.348, B:R.348, B:R.349, B:R.349 Salt bridges: A:D.176, B:K.301, B:R.348 pi-Cation interactions: A:F.178 GNP.3: 21 residues within 4Å: Chain B: D.176, L.177, F.178, P.203, G.204, V.205, G.206, K.207, T.208, F.209, F.367, H.407, S.408, C.411, C.412 Chain C: E.298, K.301, A.345, R.348, R.349 Ligands: MG.4 25 PLIP interactions: 8 interactions with chain C, 17 interactions with chain B Hydrogen bonds: C:A.345, C:R.348, C:R.348, C:R.348, C:R.349, C:R.349, B:D.176, B:F.178, B:G.204, B:V.205, B:G.206, B:K.207, B:K.207, B:T.208, B:T.208, B:F.209, B:H.407, B:S.408 Salt bridges: C:K.301, C:R.348, B:D.176 pi-Stacking: B:F.178, B:F.209, B:F.209, B:H.407 GNP.5: 21 residues within 4Å: Chain C: D.176, L.177, F.178, P.203, G.204, V.205, G.206, K.207, T.208, F.209, N.333, H.407, S.408, C.411, C.412 Chain D: E.298, K.301, A.345, R.348, R.349 Ligands: MG.6 23 PLIP interactions: 16 interactions with chain C, 7 interactions with chain D Hydrogen bonds: C:D.176, C:F.178, C:G.204, C:V.205, C:G.206, C:K.207, C:K.207, C:T.208, C:T.208, C:F.209, C:S.408, C:S.408, D:R.348, D:R.348, D:R.348, D:R.349, D:R.349 Salt bridges: C:D.176, D:K.301, D:R.348 pi-Stacking: C:F.178, C:F.209 pi-Cation interactions: C:F.209 GNP.7: 23 residues within 4Å: Chain G: D.176, L.177, F.178, P.203, G.204, V.205, G.206, K.207, T.208, F.209, D.279, E.280, N.333, H.407, S.408, C.411, C.412 Chain H: E.298, K.301, A.345, R.348, R.349 Ligands: MG.8 20 PLIP interactions: 14 interactions with chain G, 6 interactions with chain H Hydrogen bonds: G:F.178, G:P.202, G:G.204, G:V.205, G:G.206, G:K.207, G:K.207, G:T.208, G:T.208, G:F.209, G:E.280, G:H.407, H:E.298, H:R.348, H:R.348, H:R.349, H:R.349 Salt bridges: G:D.176, H:K.301 pi-Cation interactions: G:F.178 GNP.9: 22 residues within 4Å: Chain H: D.176, L.177, F.178, P.203, G.204, V.205, G.206, K.207, T.208, F.209, E.280, F.367, H.407, S.408, C.411, C.412 Chain I: E.298, D.300, K.301, R.348, R.349 Ligands: MG.10 20 PLIP interactions: 16 interactions with chain H, 4 interactions with chain I Hydrogen bonds: H:D.176, H:F.178, H:G.204, H:V.205, H:G.206, H:K.207, H:K.207, H:T.208, H:T.208, H:F.209, H:E.280, I:D.300, I:R.348, I:R.349 Salt bridges: H:D.176, I:K.301 pi-Stacking: H:F.178, H:F.209, H:F.209 pi-Cation interactions: H:H.407 GNP.11: 23 residues within 4Å: Chain I: D.176, L.177, F.178, P.202, P.203, G.204, V.205, G.206, K.207, T.208, F.209, E.280, H.407, S.408, C.411, C.412 Chain J: E.298, D.300, K.301, A.345, R.348, R.349 Ligands: MG.12 21 PLIP interactions: 16 interactions with chain I, 5 interactions with chain J Hydrogen bonds: I:D.176, I:F.178, I:G.204, I:V.205, I:G.206, I:K.207, I:K.207, I:T.208, I:T.208, I:F.209, I:E.280, I:E.280, I:S.408, J:R.348, J:R.348, J:R.349, J:R.349 Salt bridges: I:D.176, J:K.301 pi-Stacking: I:F.178, I:H.407

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: K.207, T.208, D.279, L.331 Chain B: R.349 Ligands: GNP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.208, A:D.279 MG.4: 4 residues within 4Å: Chain B: T.208, D.279 Chain C: R.349 Ligands: GNP.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.208, B:D.279 MG.6: 4 residues within 4Å: Chain C: K.207, T.208, D.279 Ligands: GNP.5 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.208, C:D.279 MG.8: 5 residues within 4Å: Chain G: T.208, D.279, L.331 Chain H: R.349 Ligands: GNP.7 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:T.208, G:D.279 MG.10: 5 residues within 4Å: Chain H: K.207, T.208, D.279 Chain I: R.349 Ligands: GNP.9 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:T.208, H:D.279 MG.12: 4 residues within 4Å: Chain I: K.207, T.208, D.279 Ligands: GNP.11 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:T.208, I:D.279

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saikrishnan, K. et al., Structure of McrBC (stalkless mutant). To Be Published

Release Date

2023-02-15

Peptides

5-methylcytosine-specific restriction enzyme B: ABCDEFGHIJKL
Protein McrC: MN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

5-methylcytosine-specific restriction enzyme B

Protein McrC