SMTL ID : 1u56.3 (2 other biounits)

Crystal structure of an oxygen binding H-NOX domain related to soluble guanylate cyclases (Water-ligated, ferric form)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 25 residues within 4Å: Chain A: M.1, K.2, I.5, F.78, Y.85, F.86, F.94, M.98, H.102, L.105, T.106, T.113, P.114, P.115, L.117, M.129, Y.131, S.133, R.135, M.137, Y.140, F.141, L.144, I.145, S.148 30 PLIP interactions: 29 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:K.2, A:I.5, A:I.5, A:F.78, A:F.78, A:Y.85, A:F.86, A:F.94, A:L.105, A:T.106, A:P.115, A:L.117, A:Y.131, A:F.141, A:F.141, A:F.141, A:I.145 Hydrogen bonds: A:K.2, A:Y.131, A:S.133 Water bridges: A:T.113, A:K.134, A:R.135, A:R.135, A:R.135 Salt bridges: A:R.135, A:R.135 pi-Stacking: A:Y.140 Metal complexes: A:H.102, H2O.1 HEM.3: 23 residues within 4Å: Chain B: M.1, K.2, I.5, F.78, Y.85, F.86, F.94, M.98, H.102, L.105, A.112, T.113, P.114, P.115, L.117, Y.131, S.133, R.135, M.137, Y.140, F.141, L.144, I.145 27 PLIP interactions: 26 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:I.5, B:F.78, B:F.78, B:Y.85, B:F.86, B:F.94, B:F.94, B:L.105, B:P.114, B:P.115, B:L.117, B:Y.131, B:Y.140, B:Y.140, B:F.141, B:F.141, B:I.145 Hydrogen bonds: B:K.2, B:T.113, B:Y.131, B:S.133 Salt bridges: B:R.135, B:R.135 pi-Stacking: B:F.78, B:Y.140 Metal complexes: B:H.102, H2O.6

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

CL.2: 6 residues within 4Å: Chain A: K.2, T.4, P.39 Chain B: F.82, P.83, S.84 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pellicena, P. et al., Crystal structure of an oxygen-binding heme domain related to soluble guanylate cyclases. Proc.Natl.Acad.Sci.Usa (2004)

Release Date

2004-08-31

Peptides

Heme-based Methyl-accepting chemotaxis protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Heme-based Methyl-accepting chemotaxis protein

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