SMTL ID : 5dgk.1

SCCmec type IV Cch - active helicase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.89 Å

Oligo State

homo-hexamer

Ligands

6 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 24 residues within 4Å: Chain A: S.212, S.213, T.214, G.215, K.216, S.217, T.218, E.264, T.308, E.310, Q.333, T.335, T.336, N.337, A.338, A.341, D.342, K.345 Chain D: G.322, R.326, N.391, I.394, R.395 Ligands: MG.2 18 PLIP interactions: 13 interactions with chain A, 5 interactions with chain D Hydrogen bonds: A:S.212, A:S.213, A:T.214, A:T.214, A:G.215, A:K.216, A:K.216, A:S.217, A:T.218, A:T.218, A:T.335, A:T.336, D:R.326, D:R.395 Salt bridges: A:K.345, D:R.395 Water bridges: D:R.395, D:R.395 ANP.3: 24 residues within 4Å: Chain A: G.322, R.326, N.391, I.394, R.395 Chain B: S.212, S.213, T.214, G.215, K.216, S.217, T.218, E.264, T.308, E.310, Q.333, T.335, T.336, N.337, A.338, A.341, D.342, K.345 Ligands: MG.4 20 PLIP interactions: 15 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:S.212, B:S.213, B:T.214, B:T.214, B:G.215, B:G.215, B:K.216, B:K.216, B:S.217, B:T.218, B:T.218, B:T.335, B:N.337, A:R.326, A:R.395, A:R.395 Water bridges: B:S.217, A:R.395 Salt bridges: B:K.345, A:R.395 ANP.5: 24 residues within 4Å: Chain C: S.212, S.213, T.214, G.215, K.216, S.217, T.218, E.264, T.308, E.310, Q.333, T.335, T.336, N.337, A.338, A.341, D.342, K.345 Chain F: G.322, R.326, N.391, I.394, R.395 Ligands: MG.6 18 PLIP interactions: 13 interactions with chain C, 5 interactions with chain F Hydrogen bonds: C:S.212, C:S.213, C:T.214, C:T.214, C:G.215, C:K.216, C:K.216, C:S.217, C:T.218, C:T.218, C:T.335, C:T.336, F:R.326, F:R.395 Salt bridges: C:K.345, F:R.395 Water bridges: F:R.395, F:R.395 ANP.7: 24 residues within 4Å: Chain C: G.322, R.326, N.391, I.394, R.395 Chain D: S.212, S.213, T.214, G.215, K.216, S.217, T.218, E.264, T.308, E.310, Q.333, T.335, T.336, N.337, A.338, A.341, D.342, K.345 Ligands: MG.8 20 PLIP interactions: 15 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:S.212, D:S.213, D:T.214, D:T.214, D:G.215, D:G.215, D:K.216, D:K.216, D:S.217, D:T.218, D:T.218, D:T.335, D:N.337, C:R.326, C:R.395, C:R.395 Water bridges: D:S.217, C:R.395 Salt bridges: D:K.345, C:R.395 ANP.9: 24 residues within 4Å: Chain B: G.322, R.326, N.391, I.394, R.395 Chain E: S.212, S.213, T.214, G.215, K.216, S.217, T.218, E.264, T.308, E.310, Q.333, T.335, T.336, N.337, A.338, A.341, D.342, K.345 Ligands: MG.10 18 PLIP interactions: 13 interactions with chain E, 5 interactions with chain B Hydrogen bonds: E:S.212, E:S.213, E:T.214, E:T.214, E:G.215, E:K.216, E:K.216, E:S.217, E:T.218, E:T.218, E:T.335, E:T.336, B:R.326, B:R.395 Salt bridges: E:K.345, B:R.395 Water bridges: B:R.395, B:R.395 ANP.11: 24 residues within 4Å: Chain E: G.322, R.326, N.391, I.394, R.395 Chain F: S.212, S.213, T.214, G.215, K.216, S.217, T.218, E.264, T.308, E.310, Q.333, T.335, T.336, N.337, A.338, A.341, D.342, K.345 Ligands: MG.12 20 PLIP interactions: 15 interactions with chain F, 5 interactions with chain E Hydrogen bonds: F:S.212, F:S.213, F:T.214, F:T.214, F:G.215, F:G.215, F:K.216, F:K.216, F:S.217, F:T.218, F:T.218, F:T.335, F:N.337, E:R.326, E:R.395, E:R.395 Water bridges: F:S.217, E:R.395 Salt bridges: F:K.345, E:R.395

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: S.217, T.308 Chain D: R.326 Ligands: ANP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.217, H2O.1, H2O.1, H2O.1 MG.4: 5 residues within 4Å: Chain A: R.326 Chain B: S.217, D.263, T.308 Ligands: ANP.3 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.217, H2O.1, H2O.1, H2O.1 MG.6: 4 residues within 4Å: Chain C: S.217, T.308 Chain F: R.326 Ligands: ANP.5 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:S.217, H2O.1, H2O.1, H2O.1 MG.8: 5 residues within 4Å: Chain C: R.326 Chain D: S.217, D.263, T.308 Ligands: ANP.7 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:S.217, H2O.1, H2O.2, H2O.2 MG.10: 4 residues within 4Å: Chain B: R.326 Chain E: S.217, T.308 Ligands: ANP.9 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:S.217, H2O.2, H2O.2, H2O.2 MG.12: 5 residues within 4Å: Chain E: R.326 Chain F: S.217, D.263, T.308 Ligands: ANP.11 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:S.217, H2O.2, H2O.2, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mir-Sanchis, I. et al., Staphylococcal SCCmec elements encode an active MCM-like helicase and thus may be replicative. Nat.Struct.Mol.Biol. (2016)

Release Date

2016-08-24

Peptides

Active helicase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Active helicase