SMTL ID : 2olp.1

Structure and ligand selection of hemoglobin II from Lucina pectinata

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: R.13, S.17 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.17 Salt bridges: A:R.13 SO4.4: 6 residues within 4Å: Chain B: X.1, T.2, T.3, K.9, L.81, N.84 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.3, B:L.81, B:N.84 Water bridges: B:N.84 Salt bridges: B:K.9

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

HEM.2: 20 residues within 4Å: Chain A: T.41, P.44, F.45, L.48, Q.66, V.69, F.70, M.74, M.94, L.97, H.98, R.101, I.103, D.107, L.108, A.111, Y.112 Chain B: K.93, L.97 Ligands: OXY.3 21 PLIP interactions: 17 interactions with chain A, 4 interactions with chain B, Hydrophobic interactions: A:T.41, A:P.44, A:P.44, A:F.45, A:F.45, A:F.45, A:L.48, A:V.69, A:F.70, A:I.103, A:Y.112, A:Y.112 Water bridges: A:L.48, A:H.98, B:K.96, B:K.96 Salt bridges: A:H.98, A:R.101, B:K.93, B:K.96 Metal complexes: A:H.98 HEM.5: 21 residues within 4Å: Chain A: K.93, L.97 Chain B: T.41, P.44, F.45, L.48, Q.66, V.69, F.70, G.73, M.74, M.94, L.97, H.98, R.101, I.103, D.107, L.108, A.111, Y.112 Ligands: OXY.6 25 PLIP interactions: 20 interactions with chain B, 5 interactions with chain A, Hydrophobic interactions: B:T.41, B:P.44, B:P.44, B:F.45, B:F.45, B:F.45, B:L.48, B:V.69, B:F.70, B:L.97, B:I.103, B:A.111, B:Y.112, B:Y.112 Water bridges: B:L.48, B:H.98, A:K.96, A:K.96, A:K.96 Salt bridges: B:H.98, B:R.101, A:K.93, A:K.96 pi-Cation interactions: B:R.101 Metal complexes: B:H.98

2 x OXY: OXYGEN MOLECULE(Non-covalent)(Covalent)

OXY.3: 5 residues within 4Å: Chain A: Y.31, F.45, Q.66, F.70 Ligands: HEM.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.31, A:Q.66 OXY.6: 5 residues within 4Å: Chain B: Y.31, F.45, Q.66, H.98 Ligands: HEM.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gavira, J.A. et al., Structure and Ligand Selection of Hemoglobin II from Lucina pectinata. J.Biol.Chem. (2008)

Release Date

2007-12-18

Peptides

Hemoglobin II: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Hemoglobin II

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