SMTL ID : 5nmo.1

Structure of the Bacillus subtilis Smc Joint domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

10 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 2 residues within 4Å: Chain A: R.7, E.9 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.7 SO4.2: 6 residues within 4Å: Chain A: E.43, L.46, T.47, D.50, L.97, Y.100 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.47, A:T.47 Water bridges: A:E.43, A:R.126 SO4.3: 4 residues within 4Å: Chain A: K.37, H.41, Y.116 Chain B: K.130 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.116, A:Y.116 Water bridges: A:E.40, A:H.41 Salt bridges: A:K.37, A:H.41, B:K.130 SO4.4: 4 residues within 4Å: Chain A: Y.32, G.140, T.141, V.142 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.142 SO4.5: 5 residues within 4Å: Chain A: K.23, A.26, S.27, K.30, F.150 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.23, A:K.30 SO4.6: 6 residues within 4Å: Chain A: V.42, A.45, L.118, E.119, T.120, R.128 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.119, A:E.119, A:T.120 Salt bridges: A:R.128 SO4.7: 5 residues within 4Å: Chain A: I.44, Y.105, L.107, Y.116 Chain B: K.130 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:K.130 Hydrogen bonds: A:Y.105 SO4.15: 5 residues within 4Å: Chain A: F.109, K.113 Chain B: K.86, R.89 Ligands: EDO.23 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Salt bridges: A:K.113, B:K.86, B:R.89 Water bridges: B:R.89, B:R.89 SO4.16: 7 residues within 4Å: Chain A: L.33, L.144, I.147, D.148 Chain B: L.134, E.138 Ligands: EDO.21 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:I.147, A:D.148 Hydrogen bonds: B:E.138 SO4.17: 3 residues within 4Å: Chain B: K.113, E.114, Q.117 No protein-ligand interaction detected (PLIP)

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.8: 8 residues within 4Å: Chain A: W.58, E.91, L.94, D.95 Chain B: V.92, D.95, N.96, Q.99 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:W.58, A:E.91, B:V.92 Hydrogen bonds: A:D.95, B:N.96, B:Q.99 MPD.18: 4 residues within 4Å: Chain B: D.95, L.98, Q.99, R.102 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.98

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.9: 4 residues within 4Å: Chain A: L.131, L.134, A.135, E.138 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.135 PEG.10: 1 residues within 4Å: Chain A: L.134 No protein-ligand interaction detected (PLIP) PEG.19: 1 residues within 4Å: Chain B: D.82 No protein-ligand interaction detected (PLIP) PEG.20: 7 residues within 4Å: Chain B: K.64, A.68, S.74, S.77, L.79, L.80, E.83 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.64

7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.11: 2 residues within 4Å: Chain A: Y.49, L.118 No protein-ligand interaction detected (PLIP) EDO.12: 3 residues within 4Å: Chain A: N.96, Q.99, E.103 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.103 Water bridges: B:E.104 EDO.13: 1 residues within 4Å: Chain A: E.137 No protein-ligand interaction detected (PLIP) EDO.14: 5 residues within 4Å: Chain A: K.36, L.39, K.133, I.136, E.137 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.133 EDO.21: 6 residues within 4Å: Chain A: D.148 Chain B: K.35, L.134, A.135, E.138 Ligands: SO4.16 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.138 EDO.22: 5 residues within 4Å: Chain B: K.23, A.26, S.27, K.30, F.150 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.23, B:K.30 EDO.23: 6 residues within 4Å: Chain A: E.110 Chain B: L.54, K.57, K.86, M.90 Ligands: SO4.15 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.86 Water bridges: B:K.57, A:E.110

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Diebold-Durand, M.L. et al., Structure of Full-Length SMC and Rearrangements Required for Chromosome Organization. Mol. Cell (2017)

Release Date

2017-06-21

Peptides

Chromosome partition protein Smc,Chromosome partition protein Smc: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Chromosome partition protein Smc,Chromosome partition protein Smc