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SMTL ID : 4xs0.1

Human methemoglobin in complex with the second and third NEAT domains of IsdH(F365Y/A369F/Y642A) from Staphylococcus aureus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

HEM.1:

21 residues within 4Å:

Chain A: T.39, Y.42, F.43, H.45, F.46, H.58, K.61, V.62, A.65, L.83, L.86, H.87, A.88, H.89, V.93, N.97, F.98, L.101, L.105, L.136
Chain C: Y.322

26 PLIP interactions:

24 interactions with chain A, 1 interactions with chain C, 1 Ligand-Water interactions,

Hydrophobic interactions: A:Y.42, A:F.43, A:F.43, A:F.46, A:V.62, A:V.62, A:A.65, A:L.83, A:L.83, A:A.88, A:V.93, A:F.98, A:L.101, A:L.105, A:L.136
Hydrogen bonds: A:A.88, C:Y.322
Salt bridges: A:H.45, A:H.89
pi-Stacking: A:H.58, A:H.58, A:H.87, A:H.87
pi-Cation interactions: A:H.87
Metal complexes: A:H.87, H₂O.1

HEM.2:

17 residues within 4Å:

Chain B: T.38, F.41, F.42, F.45, H.63, K.66, V.67, A.70, F.85, L.88, H.92, L.96, V.98, N.102, F.103, L.106, L.141

23 PLIP interactions:

22 interactions with chain B, 1 Ligand-Water interactions,

Hydrophobic interactions: B:T.38, B:F.41, B:F.41, B:F.42, B:F.42, B:K.66, B:V.67, B:V.67, B:A.70, B:F.85, B:L.88, B:L.96, B:V.98, B:N.102, B:F.103, B:L.106, B:L.141
Salt bridges: B:K.66
pi-Stacking: B:H.63, B:H.92, B:H.92
Metal complexes: B:H.92, H₂O.1

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

CL.3:	1 residues within 4Å: Chain B: N.108 Ligand excluded by PLIP
CL.4:	2 residues within 4Å: Chain A: H.72 Chain C: K.67 Ligand excluded by PLIP
CL.5:	3 residues within 4Å: Chain C: K.164, T.165, R.168 Ligand excluded by PLIP

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.6:

4 residues within 4Å:

Chain C: D.301, K.302, A.303, V.304

3 PLIP interactions:

3 interactions with chain C

Hydrogen bonds: C:A.303, C:V.304
Salt bridges: C:K.302

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Dickson, C.F. et al., The structure of haemoglobin bound to the haemoglobin receptor IsdH from Staphylococcus aureus shows disruption of the native alpha-globin haem pocket. Acta Crystallogr.,Sect.D (2015)

Release Date

2015-06-03

Peptides

Hemoglobin subunit alpha: A
Hemoglobin subunit beta: B
Iron-regulated surface determinant protein H: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Hemoglobin subunit alpha

Hemoglobin subunit beta

Iron-regulated surface determinant protein H

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