SMTL ID : 4hrr.2 (1 other biounit)

Scapharca tetrameric hemoglobin, CO-state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

hetero-2-2-mer

Ligands

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

HEM.1: 20 residues within 4Å: Chain A: T.48, Y.51, F.52, R.54, L.55, H.70, L.74, A.77, L.78, F.98, N.101, H.102, R.105, I.107, A.111, F.112, I.115 Chain B: K.99, N.103 Ligands: CMO.2 31 PLIP interactions: 25 interactions with chain A, 5 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: A:T.48, A:Y.51, A:F.52, A:F.52, A:F.52, A:L.74, A:A.77, A:F.98, A:N.101, A:R.105, A:R.105, A:I.107, A:I.107, A:F.112, A:F.112, A:I.115, A:I.115 Water bridges: A:N.101, A:N.101, A:R.105, A:R.105, B:K.99, B:K.99 Salt bridges: A:R.54, A:R.105, A:R.105, B:K.99, B:K.99 Metal complexes: A:H.102, CMO.2 Hydrogen bonds: B:N.103 HEM.3: 19 residues within 4Å: Chain A: K.97, N.101 Chain B: K.53, F.54, R.56, L.57, H.72, L.76, A.79, L.80, F.100, N.103, H.104, R.107, I.109, E.113, F.114, I.117 Ligands: CMO.4 29 PLIP interactions: 24 interactions with chain B, 4 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: B:K.53, B:F.54, B:F.54, B:F.54, B:F.100, B:N.103, B:R.107, B:R.107, B:F.114, B:F.114, B:I.117, B:I.117 Water bridges: B:F.54, B:N.103, B:N.103, B:R.107, B:R.107, B:R.107, B:R.107, B:R.107, A:K.97, A:R.105 Salt bridges: B:R.56, B:R.107, B:R.107, A:K.97 Metal complexes: B:H.104, CMO.4 Hydrogen bonds: A:N.101 HEM.5: 21 residues within 4Å: Chain C: Y.51, F.52, R.54, H.70, T.73, L.74, A.77, L.78, F.81, F.98, N.101, H.102, R.105, I.107, A.111, F.112, I.115 Chain D: K.99, N.103 Ligands: CMO.6, HEM.7 22 PLIP interactions: 15 interactions with chain C, 6 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: C:Y.51, C:Y.51, C:F.52, C:F.52, C:F.52, C:L.74, C:L.78, C:F.81, C:F.98, C:F.112, C:F.112, C:I.115 Salt bridges: C:R.54, C:R.105, D:K.99 Metal complexes: C:H.102, CMO.6 Hydrogen bonds: D:N.103 Water bridges: D:K.99, D:K.99, D:K.99, D:R.107 HEM.7: 18 residues within 4Å: Chain C: K.97, N.101 Chain D: K.53, F.54, R.56, H.72, L.76, A.79, N.103, H.104, R.107, I.109, E.113, F.114, E.116, I.117 Ligands: HEM.5, CMO.8 24 PLIP interactions: 19 interactions with chain D, 4 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: D:F.54, D:F.54, D:F.54, D:F.54, D:L.76, D:I.109, D:F.114, D:F.114, D:I.117, D:I.117 Hydrogen bonds: D:N.103, C:N.101 Water bridges: D:K.53, D:F.54, D:R.56, D:R.56, C:K.97 Salt bridges: D:R.56, D:R.107, D:R.107, C:K.97, C:K.97 Metal complexes: D:H.104, CMO.8

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

CMO.2: 6 residues within 4Å: Chain A: M.38, F.52, H.70, L.74, H.102 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.70 CMO.4: 6 residues within 4Å: Chain B: M.40, F.54, H.72, L.76, H.104 Ligands: HEM.3 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.72 CMO.6: 4 residues within 4Å: Chain C: F.52, H.70, H.102 Ligands: HEM.5 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.70 CMO.8: 6 residues within 4Å: Chain D: M.40, F.54, H.72, L.76, H.104 Ligands: HEM.7 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.72

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ronda, L. et al., Tertiary and Quaternary Allostery in Tetrameric Hemoglobin from Scapharca inaequivalvis. Biochemistry (2013)

Release Date

2013-03-13

Peptides

Globin-2 A chain: AC
Hemoglobin B chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

C
G

B
F

D
H

Globin-2 A chain

Hemoglobin B chain

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