SMTL ID : 1k0y.1

X-ray Crystallographic Analyses of Symmetrical Allosteric Effectors of Hemoglobin. Compounds Designed to Link Primary and Secondary Binding Sites

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

hetero-2-2-mer

Ligands

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

HEM.1: 18 residues within 4Å: Chain A: T.39, 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.136 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:Y.42, A:F.43, A:F.43, A:K.61, A:A.65, A:L.83, A:L.86, A:L.91, A:L.91, A:V.93, A:V.93, A:F.98, A:L.101, A:L.136 Salt bridges: A:H.45, A:K.61 pi-Stacking: A:H.58 Metal complexes: A:H.87 HEM.3: 18 residues within 4Å: Chain B: L.31, F.41, F.42, H.63, K.66, V.67, A.70, F.71, F.85, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, L.141 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:F.41, B:F.41, B:F.42, B:F.42, B:K.66, B:V.67, B:F.71, B:F.85, B:L.88, B:L.91, B:L.96, B:L.96, B:V.98, B:V.98, B:F.103, B:L.141 Salt bridges: B:K.66 pi-Stacking: B:H.63 Metal complexes: B:H.92 HEM.4: 17 residues within 4Å: Chain C: T.39, Y.42, F.43, H.45, F.46, H.58, K.61, A.65, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, L.136 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:Y.42, C:F.43, C:K.61, C:K.61, C:A.65, C:L.86, C:L.91, C:L.91, C:V.93, C:V.93, C:F.98, C:F.98, C:L.101, C:L.136 Salt bridges: C:H.45, C:K.61 pi-Stacking: C:H.58 Metal complexes: C:H.87 HEM.6: 15 residues within 4Å: Chain D: L.31, F.41, F.42, H.63, K.66, V.67, A.70, L.88, H.92, L.96, V.98, N.102, F.103, L.106, L.141 17 PLIP interactions: 17 interactions with chain D, Hydrophobic interactions: D:L.31, D:F.41, D:F.41, D:F.42, D:F.42, D:V.67, D:L.88, D:L.96, D:L.96, D:V.98, D:V.98, D:F.103, D:L.106, D:L.141 Salt bridges: D:K.66 pi-Stacking: D:H.63 Metal complexes: D:H.92

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

SO4.2: 6 residues within 4Å: Chain B: V.1, L.78, D.79, N.80, L.81, K.82 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.1, B:L.78, B:L.81, B:K.82 SO4.5: 6 residues within 4Å: Chain D: V.1, L.78, D.79, N.80, L.81, K.82 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:V.1, D:L.81, D:K.82

2 x CNO: 2-{4-[(3{2-[4-(1-CARBOXY-1-METHYL-ETHOXY)-PHENYL]-ACETYLAMINO}-PHENYLCARBAMOYL)-METHYL]-PHENOXY}-2-METHYL-PROPIONIC ACID(Non-covalent)

CNO.7: 16 residues within 4Å: Chain A: T.38, V.96, K.99, L.100, H.103 Chain B: Y.35, W.37, R.104, N.108 Chain C: P.95, T.137, R.141 Chain D: D.99, P.100, E.101, R.104 17 PLIP interactions: 5 interactions with chain B, 7 interactions with chain A, 2 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: B:Y.35, A:V.96, A:L.100, A:L.100, A:H.103, C:P.95, D:E.101 Water bridges: B:Y.35, B:Y.35, B:Y.35, B:N.108, A:K.99, C:R.141 Hydrogen bonds: A:T.38, D:R.104 pi-Cation interactions: A:K.99 Salt bridges: D:R.104 CNO.8: 14 residues within 4Å: Chain A: P.95, T.137, R.141 Chain B: D.99, P.100, E.101, R.104 Chain C: T.38, K.99, L.100, H.103 Chain D: Y.35, W.37, N.108 17 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B, 5 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: A:P.95, A:R.141, C:T.38, C:L.100, C:L.100, C:H.103, D:Y.35, D:W.37, D:W.37 Water bridges: A:R.141, D:Y.35, D:N.108, D:N.108 Salt bridges: A:R.141 Hydrogen bonds: B:E.101, B:R.104 pi-Cation interactions: C:K.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Safo, M.K. et al., X-ray crystallographic analyses of symmetrical allosteric effectors of hemoglobin: compounds designed to link primary and secondary binding sites. Acta Crystallogr.,Sect.D (2002)

Release Date

2001-10-03

Peptides

hemoglobin alpha chain: AC
hemoglobin beta chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

hemoglobin alpha chain

hemoglobin beta chain

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