SMTL ID : 4esv.1 (1 other biounit)

A New Twist on the Translocation Mechanism of Helicases from the Structure of DnaB with its Substrates

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-hexamer

Ligands

11 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.1: 2 residues within 4Å: Chain B: Q.388, D.389 No protein-ligand interaction detected (PLIP) CA.3: 6 residues within 4Å: Chain B: T.217, E.241, M.242, D.320 Ligands: GDP.2, ALF.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.217 CA.5: 2 residues within 4Å: Chain A: T.3 Chain B: S.378 No protein-ligand interaction detected (PLIP) CA.6: 6 residues within 4Å: Chain B: S.213 Chain G: A.417, K.418, Q.419, V.424 Ligands: GDP.2 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.213 CA.7: 2 residues within 4Å: Chain B: E.111, D.391 No protein-ligand interaction detected (PLIP) CA.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.10: 6 residues within 4Å: Chain D: T.217, E.241, M.242, D.320 Ligands: GDP.9, ALF.11 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.217 CA.15: 6 residues within 4Å: Chain E: T.217, E.241, M.242, D.320 Ligands: ALF.12, GDP.14 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.217 CA.17: 2 residues within 4Å: Chain E: N.232, N.285 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:N.285 CA.19: 6 residues within 4Å: Chain F: T.217, E.241, M.242, D.320 Ligands: ALF.16, GDP.18 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.217 CA.23: 6 residues within 4Å: Chain G: T.217, E.241, M.242, D.320 Ligands: ALF.20, GDP.22 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.217

5 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.2: 22 residues within 4Å: Chain B: P.212, S.213, V.214, G.215, K.216, T.217, A.218, R.250, A.260, Q.261, R.398, F.431, K.433, E.434, N.436 Chain G: Q.419, N.421, G.422, P.423 Ligands: CA.3, ALF.4, CA.6 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:S.213, B:S.213, B:S.213, B:V.214, B:G.215, B:K.216, B:T.217, B:A.218, B:Q.261, B:Q.261, B:R.264 Salt bridges: B:K.216, B:R.250, B:E.434 GDP.9: 21 residues within 4Å: Chain C: Q.419, N.421, G.422, P.423 Chain D: P.212, S.213, V.214, G.215, K.216, T.217, A.218, R.250, A.260, Q.261, R.398, F.431, K.433, E.434, N.436 Ligands: CA.10, ALF.11 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:S.213, D:S.213, D:V.214, D:G.215, D:K.216, D:T.217, D:A.218, D:Q.261, D:Q.261, D:R.398 Salt bridges: D:K.216, D:R.250 GDP.14: 23 residues within 4Å: Chain D: Q.419, R.420, N.421, G.422, P.423 Chain E: P.212, S.213, V.214, G.215, K.216, T.217, A.218, M.242, R.250, A.260, Q.261, R.264, R.398, F.431, K.433, N.436 Ligands: ALF.12, CA.15 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:S.213, E:S.213, E:S.213, E:V.214, E:G.215, E:K.216, E:T.217, E:A.218, E:Q.261, E:Q.261, E:R.264, E:R.264 Salt bridges: E:K.216, E:R.250 GDP.18: 21 residues within 4Å: Chain E: Q.419, N.421, G.422, P.423 Chain F: P.212, S.213, V.214, G.215, K.216, T.217, A.218, M.242, R.250, A.260, Q.261, R.264, F.431, K.433, N.436 Ligands: ALF.16, CA.19 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:S.213, F:S.213, F:V.214, F:G.215, F:K.216, F:T.217, F:A.218, F:Q.261, F:Q.261, F:R.264, F:R.264 Salt bridges: F:K.216, F:R.250 GDP.22: 21 residues within 4Å: Chain F: Q.419, N.421, G.422, P.423 Chain G: P.212, S.213, V.214, G.215, K.216, T.217, A.218, M.242, R.250, A.260, Q.261, R.398, F.431, K.433, N.436 Ligands: ALF.20, CA.23 13 PLIP interactions: 12 interactions with chain G, 1 interactions with chain F Hydrogen bonds: G:S.213, G:S.213, G:V.214, G:G.215, G:K.216, G:T.217, G:A.218, G:Q.261, G:Q.261, F:Q.419 Salt bridges: G:K.216, G:R.250, G:E.434

5 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.4: 10 residues within 4Å: Chain B: P.212, S.213, K.216, E.241, Q.362 Chain G: Q.388, K.418, R.420 Ligands: GDP.2, CA.3 No protein-ligand interaction detected (PLIP) ALF.11: 9 residues within 4Å: Chain C: K.418, R.420 Chain D: P.212, S.213, K.216, E.241, Q.362 Ligands: GDP.9, CA.10 No protein-ligand interaction detected (PLIP) ALF.12: 10 residues within 4Å: Chain D: Q.388, K.418, R.420 Chain E: S.213, K.216, T.217, E.241, Q.362 Ligands: GDP.14, CA.15 No protein-ligand interaction detected (PLIP) ALF.16: 10 residues within 4Å: Chain E: Q.388, K.418, R.420 Chain F: P.212, S.213, K.216, E.241, Q.362 Ligands: GDP.18, CA.19 No protein-ligand interaction detected (PLIP) ALF.20: 10 residues within 4Å: Chain F: Q.388, K.418, R.420 Chain G: P.212, S.213, K.216, E.241, Q.362 Ligands: GDP.22, CA.23 No protein-ligand interaction detected (PLIP)

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.13: 9 residues within 4Å: Chain D: S.35, E.36, I.37, L.38, I.39, D.42, R.117, K.154, H.155 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.117 Salt bridges: D:D.42 MES.21: 4 residues within 4Å: Chain F: S.13, K.112, R.116 Chain G: E.133 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:S.13, F:R.116

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Itsathitphaisarn, O. et al., The Hexameric Helicase DnaB Adopts a Nonplanar Conformation during Translocation. Cell(Cambridge,Mass.) (2012)

Release Date

2012-10-24

Peptides

Replicative helicase: BCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

C
B

D
C

E
D

F
E

G
F

Replicative helicase

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