SMTL ID : 5e6e.1

Crystal Structure of Carbonmonoxy Sickle Hemoglobin in R-State Conformation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

hetero-2-2-mer

Ligands

4 x CMO: CARBON MONOXIDE(Non-functional Binders)

CMO.1: 6 residues within 4Å: Chain A: L.29, F.43, H.58, V.62, H.87 Ligands: HEM.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.58 CMO.6: 5 residues within 4Å: Chain B: L.28, H.63, V.67, H.92 Ligands: HEM.7 No protein-ligand interaction detected (PLIP) CMO.8: 6 residues within 4Å: Chain C: L.29, F.43, H.58, V.62, H.87 Ligands: HEM.9 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.58 CMO.13: 5 residues within 4Å: Chain D: L.28, H.63, V.67, H.92 Ligands: HEM.14 No protein-ligand interaction detected (PLIP)

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

HEM.2: 19 residues within 4Å: Chain A: Y.42, F.43, H.45, F.46, H.58, K.61, A.65, L.66, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, L.105, L.136 Ligands: CMO.1 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:Y.42, A:Y.42, A:Y.42, A:F.43, A:F.46, A:L.66, A:L.83, A:L.86, A:L.91, A:V.93, A:F.98, A:L.101, A:L.105, A:L.136 Water bridges: A:H.58, A:K.61, A:K.61, A:K.61 Salt bridges: A:H.45, A:H.58 pi-Stacking: A:H.87 Metal complexes: A:H.87 HEM.7: 18 residues within 4Å: Chain B: T.38, F.41, F.42, H.63, K.66, V.67, A.70, F.71, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, L.141 Ligands: CMO.6 20 PLIP interactions: 19 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:T.38, B:F.41, B:F.41, B:F.42, B:F.42, B:V.67, B:V.67, B:F.71, B:F.71, B:L.88, B:L.96, B:V.98, B:V.98, B:N.102, B:L.141 Water bridges: B:H.63, B:K.66, B:K.66 Metal complexes: B:H.92, CMO.6 HEM.9: 19 residues within 4Å: Chain C: Y.42, F.43, H.45, F.46, H.58, K.61, A.65, L.66, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, L.105, L.136 Ligands: CMO.8 22 PLIP interactions: 22 interactions with chain C, Hydrophobic interactions: C:Y.42, C:Y.42, C:Y.42, C:F.43, C:F.46, C:L.66, C:L.83, C:L.86, C:L.91, C:V.93, C:F.98, C:L.101, C:L.105, C:L.136 Water bridges: C:H.58, C:K.61, C:K.61, C:K.61 Salt bridges: C:H.45, C:H.58 pi-Stacking: C:H.87 Metal complexes: C:H.87 HEM.14: 18 residues within 4Å: Chain D: T.38, F.41, F.42, H.63, K.66, V.67, A.70, F.71, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, L.141 Ligands: CMO.13 19 PLIP interactions: 18 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:T.38, D:F.41, D:F.41, D:F.42, D:F.42, D:V.67, D:V.67, D:F.71, D:F.71, D:L.88, D:L.96, D:V.98, D:V.98, D:N.102, D:L.141 Water bridges: D:K.66, D:K.66 Metal complexes: D:H.92, CMO.13

4 x MBN: TOLUENE(Non-covalent)

MBN.3: 8 residues within 4Å: Chain A: V.10, W.14, V.17, L.66, T.67, V.70, F.128 Ligands: MBN.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.10, A:W.14, A:V.17, A:T.67, A:V.70, A:F.128 MBN.4: 8 residues within 4Å: Chain A: A.21, Y.24, G.25, A.63, L.66, L.105, L.109 Ligands: MBN.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.21, A:Y.24, A:A.63, A:L.66, A:L.105, A:L.109, A:L.109, A:L.109 MBN.10: 8 residues within 4Å: Chain C: V.10, W.14, V.17, L.66, T.67, V.70, F.128 Ligands: MBN.11 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:V.10, C:W.14, C:V.17, C:T.67, C:V.70, C:F.128 MBN.11: 8 residues within 4Å: Chain C: A.21, Y.24, G.25, A.63, L.66, L.105, L.109 Ligands: MBN.10 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:A.21, C:Y.24, C:A.63, C:L.66, C:L.105, C:L.109, C:L.109, C:L.109

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 2 residues within 4Å: Chain A: H.112 Chain B: K.120 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Water bridges: B:K.120, B:K.120, A:H.112, A:H.112, A:H.112 Salt bridges: A:H.112 PO4.12: 2 residues within 4Å: Chain C: H.112 Chain D: K.120 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Water bridges: D:K.120, D:K.120, C:H.112 Salt bridges: C:H.112

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ghatge, M.S. et al., Crystal structure of carbonmonoxy sickle hemoglobin in R-state conformation. J.Struct.Biol. (2016)

Release Date

2015-10-28

Peptides

Hemoglobin subunit alpha: AC
Hemoglobin subunit beta: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Hemoglobin subunit alpha

Hemoglobin subunit beta

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