SMTL ID : 9gma.1

MukBEF in a DNA capture state (dimer)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-2-4-4-mer

Ligands

4 x MG: MAGNESIUM ION

MG.1: 5 residues within 4Å: Chain A: K.40, S.41, E.1407 Chain B: T.1367 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.41 MG.3: 4 residues within 4Å: Chain A: S.1366, T.1367 Chain B: S.41 Ligands: ATP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.41 MG.5: 5 residues within 4Å: Chain K: K.40, S.41, E.1407 Chain L: T.1367 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:S.41 MG.7: 4 residues within 4Å: Chain K: S.1366, T.1367 Chain L: S.41 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:S.41

4 x ATP: ADENOSINE-5'-TRIPHOSPHATE

ATP.2: 23 residues within 4Å: Chain A: G.35, N.36, G.37, A.38, G.39, K.40, S.41, T.42, G.76, G.79, K.80, E.1407, R.1450 Chain B: Q.1269, R.1352, G.1363, A.1364, L.1365, S.1366, T.1367, G.1368, E.1369 Ligands: MG.1 21 PLIP interactions: 14 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:N.36, A:G.37, A:A.38, A:G.39, A:K.40, A:S.41, A:T.42, A:T.42, A:G.76, A:G.79, A:K.80, A:E.1407, B:R.1352, B:S.1366, B:S.1366, B:T.1367, B:G.1368, B:E.1369, B:E.1369 Salt bridges: A:K.40, A:K.40 ATP.4: 23 residues within 4Å: Chain A: Q.1269, R.1352, G.1363, A.1364, L.1365, S.1366, T.1367, G.1368, E.1369 Chain B: N.16, G.35, N.36, G.37, A.38, G.39, K.40, S.41, T.42, G.76, G.79, K.80, R.1450 Ligands: MG.3 21 PLIP interactions: 14 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:N.36, B:G.37, B:A.38, B:G.39, B:G.39, B:K.40, B:S.41, B:T.42, B:T.42, B:G.76, B:G.79, B:K.80, A:R.1352, A:S.1366, A:T.1367, A:T.1367, A:G.1368, A:E.1369, A:E.1369 Salt bridges: B:K.40, B:K.40 ATP.6: 23 residues within 4Å: Chain K: G.35, N.36, G.37, A.38, G.39, K.40, S.41, T.42, G.76, G.79, K.80, E.1407, R.1450 Chain L: Q.1269, R.1352, G.1363, A.1364, L.1365, S.1366, T.1367, G.1368, E.1369 Ligands: MG.5 21 PLIP interactions: 14 interactions with chain K, 7 interactions with chain L Hydrogen bonds: K:N.36, K:G.37, K:A.38, K:G.39, K:K.40, K:S.41, K:T.42, K:T.42, K:G.76, K:G.79, K:K.80, K:E.1407, L:R.1352, L:S.1366, L:S.1366, L:T.1367, L:G.1368, L:E.1369, L:E.1369 Salt bridges: K:K.40, K:K.40 ATP.8: 23 residues within 4Å: Chain K: Q.1269, R.1352, G.1363, A.1364, L.1365, S.1366, T.1367, G.1368, E.1369 Chain L: N.16, G.35, N.36, G.37, A.38, G.39, K.40, S.41, T.42, G.76, G.79, K.80, R.1450 Ligands: MG.7 21 PLIP interactions: 7 interactions with chain K, 14 interactions with chain L Hydrogen bonds: K:R.1352, K:S.1366, K:T.1367, K:T.1367, K:G.1368, K:E.1369, K:E.1369, L:N.36, L:G.37, L:A.38, L:G.39, L:G.39, L:K.40, L:S.41, L:T.42, L:T.42, L:G.76, L:G.79, L:K.80 Salt bridges: L:K.40, L:K.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Burmann, F. et al., Mechanism of DNA capture by the MukBEF SMC complex and its inhibition by a viral DNA mimic. Cell (2025)

Release Date

2025-03-26

Peptides

Chromosome partition protein MukB: ABKL
Chromosome partition protein MukF: CD
Chromosome partition protein MukE: EFMN
Acyl carrier protein: GHOP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

K
O

L
P

C
C

D
D

E
E

F
F

M
Q

N
R

G
G

H
I

O
S

P
M

Chromosome partition protein MukB

Chromosome partition protein MukF

Chromosome partition protein MukE

Acyl carrier protein

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