SMTL ID : 4d2i.1

Crystal structure of the HerA hexameric DNA translocase from Sulfolobus solfataricus bound to AMP-PNP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.84 Å

Oligo State

homo-hexamer

Ligands

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

ANP.1: 15 residues within 4Å: Chain A: T.150, G.151, S.152, G.153, K.154, S.155, N.156, V.442, G.443, K.459, I.460, D.461, M.462 Chain B: R.142 Ligands: MG.2 19 PLIP interactions: 2 interactions with chain B, 17 interactions with chain A Hydrogen bonds: B:R.142, B:R.142, A:G.151, A:S.152, A:G.153, A:K.154, A:K.154, A:S.155, A:N.156, A:K.459, A:I.460 Water bridges: A:S.155, A:S.155, A:S.155, A:S.155, A:N.156, A:N.156, A:E.355, A:E.356 ANP.3: 16 residues within 4Å: Chain B: A.149, T.150, G.151, S.152, G.153, K.154, S.155, N.156, V.442, G.443, K.459, I.460, D.461, M.462 Chain E: R.142 Ligands: MG.4 18 PLIP interactions: 14 interactions with chain B, 4 interactions with chain E Hydrogen bonds: B:G.151, B:S.152, B:G.153, B:K.154, B:K.154, B:S.155, B:N.156, B:K.459, B:I.460, E:R.142, E:R.142 Water bridges: B:S.155, B:S.155, B:S.155, B:S.470, B:S.470, E:R.381, E:R.381 ANP.5: 15 residues within 4Å: Chain C: T.150, G.151, S.152, G.153, K.154, S.155, N.156, V.442, G.443, K.459, I.460, D.461, M.462 Chain D: R.142 Ligands: MG.6 19 PLIP interactions: 17 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:G.151, C:S.152, C:G.153, C:K.154, C:K.154, C:S.155, C:N.156, C:K.459, C:I.460, D:R.142, D:R.142 Water bridges: C:S.155, C:S.155, C:S.155, C:S.155, C:N.156, C:N.156, C:E.355, C:E.356 ANP.7: 16 residues within 4Å: Chain A: R.142 Chain D: A.149, T.150, G.151, S.152, G.153, K.154, S.155, N.156, V.442, G.443, K.459, I.460, D.461, M.462 Ligands: MG.8 18 PLIP interactions: 14 interactions with chain D, 4 interactions with chain A Hydrogen bonds: D:G.151, D:S.152, D:G.153, D:K.154, D:K.154, D:S.155, D:N.156, D:K.459, D:I.460, A:R.142, A:R.142 Water bridges: D:S.155, D:S.155, D:S.155, D:S.470, D:S.470, A:R.381, A:R.381 ANP.9: 15 residues within 4Å: Chain E: T.150, G.151, S.152, G.153, K.154, S.155, N.156, V.442, G.443, K.459, I.460, D.461, M.462 Chain F: R.142 Ligands: MG.10 19 PLIP interactions: 17 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:G.151, E:S.152, E:G.153, E:K.154, E:K.154, E:S.155, E:N.156, E:K.459, E:I.460, F:R.142, F:R.142 Water bridges: E:S.155, E:S.155, E:S.155, E:S.155, E:N.156, E:N.156, E:E.355, E:E.356 ANP.11: 16 residues within 4Å: Chain C: R.142 Chain F: A.149, T.150, G.151, S.152, G.153, K.154, S.155, N.156, V.442, G.443, K.459, I.460, D.461, M.462 Ligands: MG.12 18 PLIP interactions: 14 interactions with chain F, 4 interactions with chain C Hydrogen bonds: F:G.151, F:S.152, F:G.153, F:K.154, F:K.154, F:S.155, F:N.156, F:K.459, F:I.460, C:R.142, C:R.142 Water bridges: F:S.155, F:S.155, F:S.155, F:S.470, F:S.470, C:R.381, C:R.381

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: S.155, E.180 Ligands: ANP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.155, H2O.2, H2O.2, H2O.2 MG.4: 3 residues within 4Å: Chain B: S.155, E.180 Ligands: ANP.3 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.155, H2O.4, H2O.4, H2O.4 MG.6: 3 residues within 4Å: Chain C: S.155, E.180 Ligands: ANP.5 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:S.155, H2O.6, H2O.6, H2O.6 MG.8: 3 residues within 4Å: Chain D: S.155, E.180 Ligands: ANP.7 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:S.155, H2O.8, H2O.8, H2O.8 MG.10: 3 residues within 4Å: Chain E: S.155, E.180 Ligands: ANP.9 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:S.155, H2O.10, H2O.10, H2O.10 MG.12: 3 residues within 4Å: Chain F: S.155, E.180 Ligands: ANP.11 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:S.155, H2O.12, H2O.12, H2O.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rzechorzek, N.J. et al., Structure of the Hexameric Hera ATPase Reveals a Mechanism of Translocation-Coupled DNA-End Processing in Archaea. Nat.Commun. (2014)

Release Date

2014-12-03

Peptides

HERA: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

HERA