SMTL ID : 3k93.1

Crystal structure of phage related exonuclease (YP_719632.1) from HAEMOPHILUS SOMNUS 129PT at 2.15 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-trimer

Ligands

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

NA.1: 3 residues within 4Å: Chain A: D.100, D.111, T.112 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.112, A:T.112, A:K.113, A:K.113 NA.7: 3 residues within 4Å: Chain B: D.100, D.111, T.112 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.100, B:T.112, B:T.112, B:K.113 NA.13: 3 residues within 4Å: Chain C: D.100, D.111, T.112 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.111, C:T.112, C:T.112, C:K.113

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

CL.2: 6 residues within 4Å: Chain A: C.12, S.13, R.89, G.97, E.98, Y.144 Ligand excluded by PLIP CL.3: 5 residues within 4Å: Chain A: S.115, W.116, S.120, K.131 Ligands: GOL.4 Ligand excluded by PLIP CL.8: 6 residues within 4Å: Chain B: C.12, S.13, R.89, G.97, E.98, Y.144 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain B: S.115, W.116, S.120, K.131 Ligands: GOL.10 Ligand excluded by PLIP CL.14: 6 residues within 4Å: Chain C: C.12, S.13, R.89, G.97, E.98, Y.144 Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain C: S.115, W.116, S.120, K.131 Ligands: GOL.16 Ligand excluded by PLIP

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: Y.60, S.120 Ligands: CL.3 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.117 GOL.10: 3 residues within 4Å: Chain B: Y.60, S.120 Ligands: CL.9 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.117 GOL.16: 3 residues within 4Å: Chain C: Y.60, S.120 Ligands: CL.15 1 PLIP interactions: 1 interactions with chain C Water bridges: C:D.117

6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 5 residues within 4Å: Chain A: F.47, D.48, F.50, G.51 Chain B: Q.182 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:F.47, B:Q.182 PEG.6: 7 residues within 4Å: Chain A: S.13, H.16, K.113, A.135, G.136, Y.137, Q.140 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.16, A:A.135, A:Q.140 Water bridges: A:D.111, A:K.113 PEG.11: 5 residues within 4Å: Chain B: F.47, D.48, F.50, G.51 Chain C: Q.182 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:F.47, C:Q.182 PEG.12: 7 residues within 4Å: Chain B: S.13, H.16, K.113, A.135, G.136, Y.137, Q.140 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.16, B:A.135, B:Q.140 Water bridges: B:D.111, B:K.113 PEG.17: 5 residues within 4Å: Chain A: Q.182 Chain C: F.47, D.48, F.50, G.51 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:F.47, A:Q.182 PEG.18: 7 residues within 4Å: Chain C: S.13, H.16, K.113, A.135, G.136, Y.137, Q.140 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:H.16, C:A.135, C:Q.140 Water bridges: C:D.111, C:K.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of phage related exonuclease (YP_719632.1) from HAEMOPHILUS SOMNUS 129PT at 2.15 A resolution. To be published

Release Date

2009-11-03

Peptides

phage related exonuclease: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

phage related exonuclease