SMTL ID : 3g46.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 0.91 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 21 residues within 4Å: Chain A: T.47, Y.50, F.51, R.53, H.69, L.73, A.76, 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, XE.4, XE.5 33 PLIP interactions: 27 interactions with chain A, 5 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: A:T.47, A:Y.50, A:F.51, A:L.73, A:L.73, A:A.76, A:F.97, A:N.100, A:R.104, A:I.106, A:I.106, A:F.111, A:F.111, A:I.114, A:I.114 Water bridges: A:N.100, A:N.100, A:R.104, A:R.104, A:R.104, A:R.104, A:R.104, B:K.96, B:K.96 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, CMO.2 Hydrogen bonds: B:N.100 HEM.6: 20 residues within 4Å: Chain A: K.96, N.100 Chain B: T.47, 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.7, XE.8, XE.10 32 PLIP interactions: 28 interactions with chain B, 3 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: B:T.47, B:Y.50, B:F.51, B:F.51, B:F.51, B:L.73, B:F.97, B:N.100, B:I.106, B:I.106, B:F.111, B:F.111, B:I.114 Water bridges: B:N.100, B:N.100, B:N.100, B:N.100, B:R.104, B:R.104, B:R.104, B:R.104, B:R.104, A:K.96 Salt bridges: B:R.53, B:R.104, B:R.104, A:K.96 pi-Stacking: B:H.69, B:H.101 Metal complexes: B:H.101, CMO.7 Hydrogen bonds: A:N.100

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.7: 6 residues within 4Å: Chain B: M.37, F.51, H.69, L.73, H.101 Ligands: HEM.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.69

6 x XE: XENON(Non-covalent)

XE.3: 1 residues within 4Å: Chain A: W.135 No protein-ligand interaction detected (PLIP) XE.4: 4 residues within 4Å: Chain A: L.77, F.80, V.139 Ligands: HEM.1 No protein-ligand interaction detected (PLIP) XE.5: 5 residues within 4Å: Chain A: F.80, F.97, H.101, F.111 Ligands: HEM.1 No protein-ligand interaction detected (PLIP) XE.8: 4 residues within 4Å: Chain B: L.77, F.80, V.139 Ligands: HEM.6 No protein-ligand interaction detected (PLIP) XE.9: 1 residues within 4Å: Chain B: W.135 No protein-ligand interaction detected (PLIP) XE.10: 4 residues within 4Å: Chain B: F.97, H.101, F.111 Ligands: HEM.6 No protein-ligand interaction detected (PLIP)

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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