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SMTL ID : 5ee4.1 (1 other biounit)

The crystal structure of HpuA from Kingella denitrificans in complex with human haemoglobin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1:	5 residues within 4Å: Chain A: E.269, H.278, G.282, R.304, Y.307 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.304, A:R.304 Water bridges: A:P.279, A:G.282
GOL.6:	6 residues within 4Å: Chain C: V.1, L.78, D.79, N.80, L.81, K.82 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:V.1, C:V.1, C:L.81, C:K.82

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

HEM.2:

17 residues within 4Å:

Chain B: Y.42, F.43, F.46, H.58, K.61, V.62, A.65, L.66, L.83, L.86, H.87, L.91, N.97, F.98, L.101, L.136
Ligands: OXY.3

16 PLIP interactions:

16 interactions with chain B,

Hydrophobic interactions: B:Y.42, B:Y.42, B:F.43, B:F.43, B:F.43, B:V.62, B:L.66, B:L.83, B:L.91, B:N.97, B:L.136
Water bridges: B:K.61, B:K.61
Salt bridges: B:K.61
pi-Stacking: B:H.58
Metal complexes: B:H.87

HEM.4:

18 residues within 4Å:

Chain C: T.38, F.41, F.42, H.63, K.66, V.67, F.71, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, V.137, L.141
Ligands: OXY.5

18 PLIP interactions:

18 interactions with chain C,

Hydrophobic interactions: C:T.38, C:F.41, C:F.41, C:F.42, C:F.42, C:V.67, C:F.71, C:F.71, C:L.88, C:L.91, C:L.96, C:V.98, C:N.102, C:L.106, C:V.137, C:L.141
Salt bridges: C:K.66
Metal complexes: C:H.92

2 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.3:	4 residues within 4Å: Chain B: L.29, H.58, V.62 Ligands: HEM.2 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.58
OXY.5:	4 residues within 4Å: Chain C: H.63, V.67, H.92 Ligands: HEM.4 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.63

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Wong, C.T. et al., Structural analysis of haemoglobin binding by HpuA from the Neisseriaceae family. Nat Commun (2015)

Release Date

2015-11-04

Peptides

HpuA: A
Hemoglobin subunit alpha: B
Hemoglobin subunit beta: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
D

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

HpuA

Hemoglobin subunit alpha

Hemoglobin subunit beta

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