SMTL ID : 2d5x.1

Crystal structure of carbonmonoxy horse hemoglobin complexed with L35

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

hetero-2-2-mer

Ligands

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

HEM.1: 17 residues within 4Å: Chain A: Y.42, F.43, 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 Ligands: CMO.2, L35.3 22 PLIP interactions: 21 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Y.42, A:Y.42, A:Y.42, A:F.43, A:F.43, A:K.61, A:K.61, A:A.65, A:L.83, A:L.83, A:L.86, A:L.91, A:V.93, A:F.98, A:F.98, A:L.136 Water bridges: A:K.61, A:K.61 Salt bridges: A:H.58, A:K.61 Metal complexes: A:H.87, CMO.2 HEM.4: 18 residues within 4Å: Chain B: T.38, F.41, F.42, H.63, K.66, V.67, S.70, F.71, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, L.141 Ligands: CMO.5 19 PLIP interactions: 18 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:F.71, B:F.71, B:L.88, B:L.96, B:V.98, B:N.102, B:F.103, B:L.106, B:L.141 Salt bridges: B:H.63, B:K.66 Metal complexes: B:H.92, CMO.5 HEM.7: 17 residues within 4Å: Chain C: Y.42, F.43, 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 Ligands: CMO.8, L35.9 23 PLIP interactions: 22 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: C:Y.42, C:Y.42, C:Y.42, C:F.43, C:F.43, C:K.61, C:K.61, C:A.65, C:L.83, C:L.83, C:L.86, C:L.91, C:V.93, C:F.98, C:F.98, C:L.136 Water bridges: C:H.58, C:K.61, C:K.61 Salt bridges: C:H.58, C:K.61 Metal complexes: C:H.87, CMO.8 HEM.10: 18 residues within 4Å: Chain D: T.38, F.41, F.42, H.63, K.66, V.67, S.70, F.71, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, L.141 Ligands: CMO.11 20 PLIP interactions: 19 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:F.71, D:F.71, D:L.88, D:L.96, D:V.98, D:N.102, D:F.103, D:L.106, D:L.141 Water bridges: D:H.63 Salt bridges: D:H.63, D:K.66 Metal complexes: D:H.92, CMO.11

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

CMO.2: 5 residues within 4Å: Chain A: L.29, H.58, V.62, H.87 Ligands: HEM.1 No protein-ligand interaction detected (PLIP) CMO.5: 6 residues within 4Å: Chain B: L.28, F.42, H.63, V.67, H.92 Ligands: HEM.4 No protein-ligand interaction detected (PLIP) CMO.8: 5 residues within 4Å: Chain C: L.29, H.58, V.62, H.87 Ligands: HEM.7 No protein-ligand interaction detected (PLIP) CMO.11: 6 residues within 4Å: Chain D: L.28, F.42, H.63, V.67, H.92 Ligands: HEM.10 No protein-ligand interaction detected (PLIP)

4 x L35: 2-[4-({[(3,5-DICHLOROPHENYL)AMINO]CARBONYL}AMINO)PHENOXY]-2-METHYLPROPANOIC ACID(Non-covalent)

L35.3: 9 residues within 4Å: Chain A: K.61, D.64, A.65, L.68, N.82, L.83, L.86, K.90 Ligands: HEM.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.65, A:N.82, A:L.83, A:L.86, A:L.86, A:L.86 Salt bridges: A:K.90 L35.6: 12 residues within 4Å: Chain A: F.36, K.99, L.100, H.103, D.126, S.130 Chain B: Y.35, W.37, L.105, N.108 Chain C: P.95, T.137 10 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: B:W.37, A:K.99, A:L.100, C:P.95, C:P.95 Hydrogen bonds: B:Y.35, B:Y.35 Water bridges: B:Y.35, B:N.108, C:T.137 L35.9: 9 residues within 4Å: Chain C: K.61, D.64, A.65, L.68, N.82, L.83, L.86, K.90 Ligands: HEM.7 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:A.65, C:N.82, C:L.83, C:L.86, C:L.86, C:L.86 Salt bridges: C:K.90 L35.12: 12 residues within 4Å: Chain A: P.95, T.137 Chain C: F.36, K.99, L.100, H.103, D.126, S.130 Chain D: Y.35, W.37, L.105, N.108 9 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: C:K.99, C:L.100, A:P.95, A:P.95, D:W.37 Water bridges: A:T.137, D:Y.35, D:N.108 Hydrogen bonds: D:Y.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yokoyama, T. et al., R-state haemoglobin with low oxygen affinity: crystal structures of deoxy human and carbonmonoxy horse haemoglobin bound to the effector molecule L35. J.Mol.Biol. (2006)

Release Date

2006-03-07

Peptides

Hemoglobin alpha subunit: AC
Hemoglobin beta subunit: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Hemoglobin alpha subunit

Hemoglobin beta subunit

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