SMTL ID : 3g4v.1

Ligand migration and cavities within scapharca dimeric hemoglobin: wild type with co bound to heme and chloropentane bound to the XE4 cavity

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 17 residues within 4Å: Chain A: Y.50, F.51, R.53, H.69, L.73, L.77, F.97, N.100, H.101, R.104, I.106, E.110, F.111, I.114 Chain B: K.96, N.100 Ligands: CMO.2 20 PLIP interactions: 17 interactions with chain A, 3 interactions with chain B, Hydrophobic interactions: A:Y.50, A:F.51, A:F.51, A:L.73, A:L.77, A:F.97, A:R.104, A:I.106, A:F.111, A:F.111, A:I.114, A:I.114 Salt bridges: A:R.53, A:R.104, A:R.104, B:K.96, B:K.96 pi-Stacking: A:H.69 Metal complexes: A:H.101 Hydrogen bonds: B:N.100 HEM.4: 17 residues within 4Å: Chain A: K.96, N.100 Chain B: Y.50, F.51, R.53, H.69, L.73, L.77, F.97, N.100, H.101, R.104, I.106, E.110, F.111, I.114 Ligands: CMO.5 19 PLIP interactions: 16 interactions with chain B, 3 interactions with chain A, Hydrophobic interactions: B:Y.50, B:F.51, B:F.51, B:F.97, B:R.104, B:I.106, B:F.111, B:F.111, B:I.114, B:I.114 Salt bridges: B:R.53, B:R.104, B:R.104, A:K.96 pi-Stacking: B:H.69, B:H.69 Metal complexes: B:H.101 Hydrogen bonds: A:N.100 Water bridges: A:K.96

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

CMO.2: 6 residues within 4Å: Chain A: M.37, F.51, H.69, L.73, H.101 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.69 CMO.5: 6 residues within 4Å: Chain B: M.37, F.51, H.69, L.73, H.101 Ligands: HEM.4 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.69

2 x 7CL: 1-chloropentane(Non-covalent)

7CL.3: 6 residues within 4Å: Chain A: S.21, W.22, I.25, L.36, L.122, W.135 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.22, A:I.25, A:L.36, A:W.135 7CL.6: 9 residues within 4Å: Chain B: S.21, W.22, I.25, N.32, L.36, M.74, V.121, L.122, W.135 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.25, B:L.36, B:V.121

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Knapp, J.E. et al., Ligand migration and cavities within Scapharca Dimeric HbI: studies by time-resolved crystallo-graphy, Xe binding, and computational analysis. Structure (2009)

Release Date

2009-12-01

Peptides

GLOBIN-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

GLOBIN-1

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