- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 3.20 Å
- Oligo State
- homo-hexamer
- Ligands
- 2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)
- 5 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)
GDP.2: 20 residues within 4Å:- Chain B: P.212, S.213, V.214, G.215, K.216, T.217, A.218, R.250, Q.261, R.398, F.431, K.433, E.434, N.436
- Chain G: Q.419, N.421, G.422, P.423, V.424
- Ligands: ALF.3
12 PLIP interactions:11 interactions with chain B, 1 interactions with chain G- Hydrogen bonds: B:S.213, B:S.213, B:G.215, B:K.216, B:T.217, B:T.217, B:A.218, B:Q.261, B:R.398, G:Q.419
- Salt bridges: B:K.216, B:R.250
GDP.5: 20 residues within 4Å:- Chain C: Q.419, N.421, G.422, P.423, V.424
- Chain D: P.212, S.213, V.214, G.215, K.216, T.217, A.218, R.250, A.260, Q.261, K.433, E.434, N.436
- Ligands: CA.6, ALF.7
11 PLIP interactions:11 interactions with chain D- Hydrogen bonds: D:S.213, D:S.213, D:G.215, D:K.216, D:T.217, D:A.218, D:R.250, D:Q.261, D:Q.261
- Salt bridges: D:K.216, D:R.250
GDP.9: 20 residues within 4Å:- Chain D: Q.419, N.421, G.422, V.424
- Chain E: R.211, 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: ALF.10
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:T.217, E:A.218, E:Q.261, E:Q.261, E:R.398
- Salt bridges: E:K.216, E:R.250
GDP.11: 19 residues within 4Å:- Chain E: Q.419, R.420, N.421, G.422, P.423, V.424
- Chain F: P.212, S.213, G.215, K.216, T.217, A.218, R.250, A.260, Q.261, K.433, E.434, N.436
- Ligands: ALF.12
12 PLIP interactions:12 interactions with chain F- Hydrogen bonds: F:S.213, F:S.213, F:V.214, F:K.216, F:T.217, F:T.217, F:A.218, F:A.260, F:Q.261, F:Q.261
- Salt bridges: F:K.216, F:R.250
GDP.13: 18 residues within 4Å:- Chain F: Q.419, G.422, P.423, V.424
- Chain G: P.212, S.213, G.215, K.216, T.217, A.218, R.250, Q.261, F.431, K.433, E.434, N.436
- Ligands: ALF.14, CA.15
13 PLIP interactions:12 interactions with chain G, 1 interactions with chain F- Hydrogen bonds: G:S.213, G:S.213, G:S.213, G:G.215, G:K.216, G:T.217, G:T.217, G:A.218, G:Q.261, G:R.398, F:V.424
- Salt bridges: G:K.216, G:R.250
- 5 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)
ALF.3: 10 residues within 4Å:- Chain B: P.212, K.216, T.217, E.241, M.242, Q.362
- Chain G: Q.388, K.418, R.420
- Ligands: GDP.2
No protein-ligand interaction detected (PLIP)ALF.7: 11 residues within 4Å:- Chain C: Q.388, K.418, R.420
- Chain D: K.216, T.217, E.241, M.242, Y.321, Q.362
- Ligands: GDP.5, CA.6
No protein-ligand interaction detected (PLIP)ALF.10: 10 residues within 4Å:- Chain D: Q.388, K.418, R.420
- Chain E: P.212, K.216, T.217, E.241, M.242, Q.362
- Ligands: GDP.9
No protein-ligand interaction detected (PLIP)ALF.12: 11 residues within 4Å:- Chain E: Q.388, K.418, R.420
- Chain F: P.212, S.213, K.216, T.217, E.241, M.242, Q.362
- Ligands: GDP.11
No protein-ligand interaction detected (PLIP)ALF.14: 12 residues within 4Å:- Chain F: Q.388, K.418, R.420
- Chain G: P.212, S.213, K.216, E.241, M.242, Y.321, Q.362
- Ligands: GDP.13, CA.15
No protein-ligand interaction detected (PLIP)- 3 x CA: CALCIUM ION(Non-covalent)
CA.4: 1 residues within 4Å:- Chain B: E.111
No protein-ligand interaction detected (PLIP)CA.6: 6 residues within 4Å:- Chain D: T.217, E.241, M.242, D.320
- Ligands: GDP.5, ALF.7
1 PLIP interactions:1 interactions with chain D- Metal complexes: D:T.217
CA.15: 5 residues within 4Å:- Chain G: T.217, E.241, D.320
- Ligands: GDP.13, ALF.14
1 PLIP interactions:1 interactions with chain G- Metal complexes: G:T.217
- 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
GC
HD
IE
JF
KG
L
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 3.20 Å
- Oligo State
- homo-hexamer
- Ligands
- 2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)
- 5 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)
- 5 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)
- 3 x CA: CALCIUM ION(Non-covalent)
- 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
GC
HD
IE
JF
KG
L