SMTL ID : 3gas.1 (2 other biounits)

Crystal Structure of Helicobacter pylori Heme Oxygenase Hugz in Complex with Heme

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 26 residues within 4Å: Chain A: K.23, F.24, I.162, R.166, R.219, V.221, F.224, G.225, Y.237, G.239, G.242, N.243, P.244, H.245 Chain B: V.130, S.131, V.133, A.134, H.136, G.198, T.201, I.202, M.205, F.208 Ligands: AZI.2, EDO.5 24 PLIP interactions: 18 interactions with chain A, 6 interactions with chain B, Hydrophobic interactions: A:K.23, A:F.24, A:V.221, A:F.224, A:N.243, A:P.244, B:V.133 Water bridges: A:R.166, A:R.166, A:R.166, A:R.166, A:R.168, A:R.219, B:E.135 Salt bridges: A:R.166, A:R.219, B:H.136 pi-Stacking: A:H.245, A:H.245, B:F.208 pi-Cation interactions: A:H.245 Metal complexes: A:H.245 Hydrogen bonds: B:S.131, B:S.131 HEM.6: 26 residues within 4Å: Chain A: V.130, S.131, V.133, A.134, H.136, T.201, I.202, M.205, F.208 Chain B: K.23, F.24, I.162, R.166, R.219, V.221, F.224, G.225, Y.237, V.238, G.239, G.242, N.243, P.244, H.245 Ligands: AZI.7, EDO.12 26 PLIP interactions: 19 interactions with chain B, 7 interactions with chain A, Hydrophobic interactions: B:K.23, B:F.24, B:V.221, B:F.224, B:F.224, B:V.238, B:N.243, B:P.244, A:V.133, A:T.201, A:F.208, A:F.208 Water bridges: B:R.166, B:R.166, B:R.168, B:R.168 Salt bridges: B:R.166, B:R.168, B:R.219, A:H.136 pi-Stacking: B:H.245, B:H.245 pi-Cation interactions: B:H.245 Metal complexes: B:H.245 Hydrogen bonds: A:S.131, A:S.131

2 x AZI: AZIDE ION(Non-covalent)

AZI.2: 5 residues within 4Å: Chain A: V.221, G.223, F.224, G.225 Ligands: HEM.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.225 Water bridges: A:R.166, A:R.166 AZI.7: 5 residues within 4Å: Chain B: V.221, G.223, F.224, G.225 Ligands: HEM.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.225 Water bridges: B:R.166, B:R.166

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 6 residues within 4Å: Chain A: K.124, Q.125, Y.126, L.213, D.214, F.215 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.126, A:Y.126, A:D.214, A:F.215 Water bridges: A:Q.125, A:Q.125 EDO.4: 7 residues within 4Å: Chain A: E.148, R.168, K.170, E.217, G.218, R.219 Chain B: E.135 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.148 Water bridges: A:K.170, A:G.218 EDO.5: 6 residues within 4Å: Chain A: F.24, I.55, E.56, L.74, F.224 Ligands: HEM.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.56 Water bridges: A:N.58, A:N.58, A:S.77 EDO.8: 6 residues within 4Å: Chain B: K.124, Q.125, Y.126, L.213, D.214, F.215 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.126, B:Y.126, B:F.215 Water bridges: B:Q.125, B:D.214, B:F.215 EDO.9: 7 residues within 4Å: Chain A: E.135 Chain B: E.148, R.168, K.170, E.217, G.218, R.219 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.168, B:K.170 EDO.10: 6 residues within 4Å: Chain B: K.80, D.83, G.86, V.87, E.90, K.222 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.86, B:E.90, B:K.222 EDO.11: 5 residues within 4Å: Chain A: K.200 Chain B: D.39, S.40, Q.41, R.54 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.40, B:Q.41, A:K.200 Water bridges: B:S.40, B:Q.41, B:R.54 EDO.12: 6 residues within 4Å: Chain B: F.24, I.55, E.56, L.74, F.224 Ligands: HEM.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jiang, F. et al., Crystal Structure of Helicobacter pylori Heme Oxygenase Hugz in Complex with Heme. To be Published

Release Date

2010-02-23

Peptides

heme oxygenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

heme oxygenase

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