SMTL ID : 2v79.1

Crystal Structure of the N-terminal domain of DnaD from Bacillus Subtilis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

6 x NA: SODIUM ION(Non-functional Binders)

NA.1: 3 residues within 4Å: Chain A: Q.58, M.61, I.63 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.61, A:M.61 Water bridges: A:G.60 NA.2: 4 residues within 4Å: Chain A: T.14, T.16, E.46 Chain D: T.14 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:T.14, A:T.16, A:K.42 Water bridges: D:T.14 NA.7: 3 residues within 4Å: Chain B: Q.58, M.61, I.63 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:M.61, B:I.63 Water bridges: B:Q.58, A:K.26 NA.15: 3 residues within 4Å: Chain C: Q.58, M.61, I.63 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.58, C:M.61 Water bridges: C:G.60 NA.16: 4 residues within 4Å: Chain B: T.14 Chain C: T.14, T.16, E.46 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Water bridges: B:T.14 Hydrogen bonds: C:T.16, C:K.42, C:E.46 NA.21: 3 residues within 4Å: Chain D: Q.58, M.61, I.63 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Water bridges: C:K.26, D:Q.58 Hydrogen bonds: D:Q.58, D:M.61

22 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 5 residues within 4Å: Chain A: T.16, P.18, K.42 Chain D: Q.10, T.14 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: W.103 Chain D: E.11 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: T.14 Chain D: T.16, K.42 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: L.28, F.80 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain B: Q.10, T.14 Ligands: CL.22 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: T.53, P.54, N.55 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain B: I.76, F.82, I.83 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain B: W.103 Chain C: E.11 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain B: F.94, E.95 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain B: N.31, T.33, R.71 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain B: K.40, M.43, H.44, Q.56 Ligand excluded by PLIP CL.17: 5 residues within 4Å: Chain B: Q.10, T.14 Chain C: T.16, P.18, K.42 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain B: E.11 Chain C: W.103 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain B: T.16, K.42 Chain C: T.14 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain C: L.28, F.80 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain D: Q.10, T.14 Ligands: CL.8 Ligand excluded by PLIP CL.23: 3 residues within 4Å: Chain D: T.53, P.54, N.55 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain D: I.76, F.82, I.83 Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain A: E.11 Chain D: W.103 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain D: F.94, E.95 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain D: N.31, T.33, R.71 Ligand excluded by PLIP CL.28: 4 residues within 4Å: Chain D: K.40, M.43, H.44, Q.56 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schneider, S. et al., Structure of the N-Terminal Oligomerization Domain of Dnad Reveals a Unique Tetramerization Motif and Provides Insights Into Scaffold Formation. J.Mol.Biol. (2008)

Release Date

2008-01-15

Peptides

DNA REPLICATION PROTEIN DNAD: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

DNA REPLICATION PROTEIN DNAD