SMTL ID : 6hk2.1

Crystal structure of ferric R-state human methemoglobin bound to maleimide-deferoxamine bifunctional chelator (DFO)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

hetero-2-2-mer

Ligands

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

HEM.1: 16 residues within 4Å: Chain A: Y.42, F.43, F.46, H.58, K.61, V.62, L.66, L.83, H.87, L.91, V.93, N.97, F.98, L.101, L.136 Ligands: OXY.2 21 PLIP interactions: 20 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:F.43, A:F.46, A:K.61, A:K.61, A:V.62, A:V.62, A:L.83, A:L.91, A:V.93, A:F.98, A:L.101, A:L.101, A:L.136 Water bridges: A:H.58, A:K.61, A:K.61, A:K.61 Salt bridges: A:K.61 pi-Stacking: A:H.58 Metal complexes: A:H.87, H2O.1 HEM.4: 16 residues within 4Å: Chain B: T.38, F.41, F.42, F.45, H.63, V.67, A.70, F.71, L.88, H.92, L.96, V.98, N.102, F.103, L.106, L.141 21 PLIP interactions: 20 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:F.42, B:A.70, B:L.88, B:L.96, B:L.96, B:V.98, B:V.98, B:N.102, B:F.103, B:F.103, B:L.106, B:L.141 Water bridges: B:S.44 pi-Stacking: B:H.63 Metal complexes: B:H.92, H2O.9 HEM.10: 16 residues within 4Å: Chain C: Y.42, F.43, F.46, H.58, K.61, V.62, A.65, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, L.136 12 PLIP interactions: 11 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: C:Y.42, C:Y.42, C:F.43, C:L.83, C:L.91, C:V.93, C:F.98, C:L.136 Salt bridges: C:K.61 pi-Cation interactions: C:H.87 Metal complexes: C:H.87, H2O.15 HEM.13: 16 residues within 4Å: Chain D: T.38, F.41, F.42, F.45, H.63, K.66, A.70, F.71, L.88, H.92, L.96, V.98, N.102, F.103, L.106, L.141 22 PLIP interactions: 21 interactions with chain D, 1 Ligand-Water interactions Hydrophobic interactions: D:T.38, D:F.41, D:F.41, D:F.42, D:F.42, D:K.66, D:A.70, D:F.71, D:L.88, D:L.96, D:L.96, D:V.98, D:N.102, D:F.103, D:L.106, D:L.141 Water bridges: D:H.63 Salt bridges: D:H.63, D:K.66 pi-Stacking: D:H.63 Metal complexes: D:H.92, H2O.20

1 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.2: 5 residues within 4Å: Chain A: F.43, H.58, V.62, H.87 Ligands: HEM.1 No protein-ligand interaction detected (PLIP)

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

SO4.3: 3 residues within 4Å: Chain A: H.89, R.92 Chain D: P.36 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain D Water bridges: A:R.92, A:R.92, A:R.92, A:R.92, D:Q.39 Salt bridges: A:H.89, A:R.92 SO4.6: 1 residues within 4Å: Chain B: N.19 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.19 Water bridges: B:N.19, B:N.19 Salt bridges: B:H.117 SO4.7: 3 residues within 4Å: Chain B: N.139, H.143 Chain D: N.139 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:N.139, D:N.139 Salt bridges: B:H.143 SO4.8: 2 residues within 4Å: Chain A: H.112 Chain B: K.120 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Water bridges: A:A.111, A:A.111, A:H.112, A:H.112, B:K.120 Salt bridges: A:H.112, B:K.120 SO4.9: 2 residues within 4Å: Chain B: H.116, H.117 5 PLIP interactions: 5 interactions with chain B Water bridges: B:E.26, B:R.30, B:V.113 Salt bridges: B:H.116, B:H.117 SO4.11: 2 residues within 4Å: Chain A: K.99 Chain C: K.99 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Water bridges: C:K.99, C:K.99 Salt bridges: C:K.99, A:K.99 SO4.12: 3 residues within 4Å: Chain B: P.36 Chain C: H.89, R.92 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Water bridges: B:V.33 Salt bridges: C:R.92

2 x G7Z: 3-[2,5-bis(oxidanylidene)pyrrolidin-1-yl]-~{N}-methyl-propanamide(Covalent)

G7Z.5: 4 residues within 4Å: Chain B: E.90, C.93, D.94, K.144 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.90 G7Z.14: 7 residues within 4Å: Chain B: H.2, K.132 Chain D: C.93, D.94, K.144, Y.145, H.146 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:K.144 Hydrogen bonds: D:H.146

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kiraga, L. et al., Biodistribution PET/CT Study of Hemoglobin-DFO-89Zr Complex in Healthy and Lung Tumor-Bearing Mice. Int J Mol Sci (2020)

Release Date

2019-09-18

Peptides

Hemoglobin subunit alpha: AC
Hemoglobin subunit beta: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Hemoglobin subunit alpha

Hemoglobin subunit beta

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