SMTL ID : 7q2x.1

Cryo-EM structure of clamped S.cerevisiae condensin-DNA complex (Form I)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 22 residues within 4Å: Chain A: K.12, S.13, L.33, N.34, G.35, G.37, K.38, S.39, N.40, R.58, D.64, I.66, Y.67, Q.147 Chain B: K.1315, R.1318, N.1322, S.1324, G.1325, E.1327 Ligands: BEF.2, MG.3 19 PLIP interactions: 14 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:N.34, A:G.35, A:G.35, A:G.37, A:K.38, A:S.39, A:S.39, A:N.40, A:N.40, A:R.58, A:I.66, A:Q.147, B:R.1318, B:N.1322, B:S.1324, B:G.1325 Salt bridges: A:K.38, A:K.38 pi-Cation interactions: B:R.1318 ADP.4: 24 residues within 4Å: Chain A: L.1073, K.1078, E.1083, S.1085, Q.1088 Chain B: K.165, S.166, P.186, N.187, G.188, S.189, G.190, K.191, S.192, N.193, R.210, Q.211, D.216, L.217, I.218, H.219, K.220 Ligands: BEF.5, MG.6 16 PLIP interactions: 12 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:G.188, B:S.189, B:G.190, B:K.191, B:S.192, B:N.193, B:N.193, B:Q.211, B:I.218, B:K.220, A:K.1078, A:S.1085, A:Q.1088, A:Q.1088 Salt bridges: B:K.191, B:R.210

2 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.2: 11 residues within 4Å: Chain A: N.34, K.38, Q.147, E.1113, L.1144 Chain B: S.1324, G.1325, G.1326, A.1356 Ligands: ADP.1, MG.3 No protein-ligand interaction detected (PLIP) BEF.5: 10 residues within 4Å: Chain A: S.1085, G.1087, A.1117 Chain B: N.187, G.188, K.191, Q.302, L.1383 Ligands: ADP.4, MG.6 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: S.39, Q.147, E.1113 Ligands: ADP.1, BEF.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.39 MG.6: 4 residues within 4Å: Chain B: S.192, Q.302 Ligands: ADP.4, BEF.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.192

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, B.G. et al., Clamping of DNA shuts the condensin neck gate. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-03-23

Peptides

Structural maintenance of chromosomes protein 2: A
Structural maintenance of chromosomes protein 4: B
Condensin complex subunit 2: C
Condensin complex subunit 1: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Structural maintenance of chromosomes protein 2

Structural maintenance of chromosomes protein 4

Condensin complex subunit 2

Condensin complex subunit 1

Related Entries With Identical Sequence