SMTL ID : 2wp0.1

Crystal structure of a HobA-DnaA (domain I-II) complex from Helicobacter pylori.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.67 Å

Oligo State

hetero-4-4-mer

Ligands

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

CL.1: 2 residues within 4Å: Chain A: N.120 Ligands: GOL.2 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: N.86, Y.91, K.93 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: R.58, E.150 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain B: N.168 Ligands: NA.9 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain B: Y.91, K.93 Ligands: NA.13 Ligand excluded by PLIP CL.17: 1 residues within 4Å: Ligands: NA.19 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain E: N.120 Ligands: GOL.22 Ligand excluded by PLIP CL.23: 3 residues within 4Å: Chain E: N.86, Y.91, K.93 Ligand excluded by PLIP CL.27: 2 residues within 4Å: Chain E: R.58, E.150 Ligand excluded by PLIP CL.28: 2 residues within 4Å: Chain F: N.168 Ligands: NA.29 Ligand excluded by PLIP CL.32: 3 residues within 4Å: Chain F: Y.91, K.93 Ligands: NA.33 Ligand excluded by PLIP CL.37: 1 residues within 4Å: Ligands: NA.39 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: I.118, E.119, N.120, E.121 Ligands: CL.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.119 GOL.10: 4 residues within 4Å: Chain B: I.118, E.119, N.120, E.121 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.118, B:E.121 GOL.22: 5 residues within 4Å: Chain E: I.118, E.119, N.120, E.121 Ligands: CL.21 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:E.119, E:E.121 GOL.30: 4 residues within 4Å: Chain F: I.118, E.119, N.120, E.121 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:I.118, F:E.121

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

NA.4: 5 residues within 4Å: Chain A: I.83, Y.107 Chain F: I.83, Y.107 Ligands: NA.34 Ligand excluded by PLIP NA.5: 1 residues within 4Å: Chain A: E.139 Ligand excluded by PLIP NA.6: 2 residues within 4Å: Chain A: Y.91, K.93 Ligand excluded by PLIP NA.9: 4 residues within 4Å: Chain A: F.11 Chain B: K.164, N.168 Ligands: CL.8 Ligand excluded by PLIP NA.11: 4 residues within 4Å: Chain B: F.18, K.149, D.152, S.153 Ligand excluded by PLIP NA.13: 5 residues within 4Å: Chain B: A.54, D.55, S.56, E.119 Ligands: CL.12 Ligand excluded by PLIP NA.14: 5 residues within 4Å: Chain B: I.83, Y.107 Chain E: I.83, Y.107 Ligands: NA.24 Ligand excluded by PLIP NA.15: 4 residues within 4Å: Chain A: N.68 Chain B: S.57, W.60, D.156 Ligand excluded by PLIP NA.16: 3 residues within 4Å: Chain B: N.68, K.164, E.167 Ligand excluded by PLIP NA.18: 1 residues within 4Å: Chain B: K.177 Ligand excluded by PLIP NA.19: 1 residues within 4Å: Ligands: CL.17 Ligand excluded by PLIP NA.24: 5 residues within 4Å: Chain B: I.83, Y.107 Chain E: I.83, Y.107 Ligands: NA.14 Ligand excluded by PLIP NA.25: 1 residues within 4Å: Chain E: E.139 Ligand excluded by PLIP NA.26: 2 residues within 4Å: Chain E: Y.91, K.93 Ligand excluded by PLIP NA.29: 4 residues within 4Å: Chain E: F.11 Chain F: K.164, N.168 Ligands: CL.28 Ligand excluded by PLIP NA.31: 4 residues within 4Å: Chain F: F.18, K.149, D.152, S.153 Ligand excluded by PLIP NA.33: 5 residues within 4Å: Chain F: A.54, D.55, S.56, E.119 Ligands: CL.32 Ligand excluded by PLIP NA.34: 5 residues within 4Å: Chain A: I.83, Y.107 Chain F: I.83, Y.107 Ligands: NA.4 Ligand excluded by PLIP NA.35: 4 residues within 4Å: Chain E: N.68 Chain F: S.57, W.60, D.156 Ligand excluded by PLIP NA.36: 3 residues within 4Å: Chain F: N.68, K.164, E.167 Ligand excluded by PLIP NA.38: 1 residues within 4Å: Chain F: K.177 Ligand excluded by PLIP NA.39: 1 residues within 4Å: Ligands: CL.37 Ligand excluded by PLIP

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.20: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ACT.40: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Natrajan, G. et al., The Structure of a Dnaa/Hoba Complex from Helicobacter Pylori Provides Insight Into Regulation of DNA Replication in Bacteria. Proc.Natl.Acad.Sci.USA (2009)

Release Date

2009-11-17

Peptides

HOBA: ABEF
CHROMOSOMAL REPLICATION INITIATOR PROTEIN DNAA: CDGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
A

F
B

C
C

D
D

G
C

H
D

HOBA

CHROMOSOMAL REPLICATION INITIATOR PROTEIN DNAA