SMTL ID : 3d17.1

A triply ligated crystal structure of relaxed state human hemoglobin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-2-2-mer

Ligands

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

HEM.1: 21 residues within 4Å: Chain A: M.32, T.39, Y.42, F.43, F.46, H.58, K.61, V.62, A.65, L.66, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, V.132, L.136 Ligands: CMO.3 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:F.43, A:F.43, A:F.43, A:V.62, A:A.65, A:L.66, A:L.66, A:L.83, A:L.86, A:L.91, A:V.93, A:F.98, A:F.98, A:L.101, A:V.132, A:L.136 Salt bridges: A:H.58, A:K.61 Metal complexes: A:H.87 HEM.6: 18 residues within 4Å: Chain B: L.31, T.38, F.41, F.42, H.63, K.66, V.67, A.70, F.71, L.91, H.92, L.96, V.98, N.102, F.103, L.106, L.141 Ligands: CMO.7 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:L.31, B:T.38, B:F.41, B:F.41, B:F.42, B:K.66, B:V.67, B:V.67, B:A.70, B:F.71, B:F.71, B:L.91, B:L.96, B:V.98, B:V.98, B:N.102, B:L.141 Salt bridges: B:H.63 Metal complexes: B:H.92 HEM.8: 17 residues within 4Å: Chain C: M.32, T.39, Y.42, F.43, F.46, H.58, K.61, V.62, A.65, L.83, H.87, L.91, V.93, N.97, F.98, L.101, L.136 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:Y.42, C:F.43, C:F.43, C:K.61, C:V.62, C:A.65, C:L.83, C:L.91, C:V.93, C:F.98, C:F.98, C:L.101, C:L.136 Salt bridges: C:H.58, C:K.61, C:K.61 Metal complexes: C:H.87 HEM.10: 15 residues within 4Å: Chain D: 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 Ligands: CMO.11 18 PLIP interactions: 18 interactions with chain D, Hydrophobic interactions: D:F.41, D:F.41, D:F.42, D:V.67, D:V.67, D:A.70, D:L.88, D:L.96, D:L.96, D:V.98, D:V.98, D:N.102, D:F.103, D:L.106, D:L.141 Salt bridges: D:H.63, D:H.63 Metal complexes: D:H.92

1 x MBN: TOLUENE(Non-covalent)

MBN.2: 6 residues within 4Å: Chain A: V.10, W.14, V.17, A.21, L.66, F.128 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.10, A:W.14, A:V.17, A:A.21, A:L.66, A:F.128 pi-Stacking: A:W.14

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

CMO.3: 6 residues within 4Å: Chain A: L.29, F.43, H.58, V.62, H.87 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.58 CMO.7: 5 residues within 4Å: Chain B: L.28, F.42, V.67, H.92 Ligands: HEM.6 No protein-ligand interaction detected (PLIP) CMO.11: 5 residues within 4Å: Chain D: L.28, F.42, V.67, H.92 Ligands: HEM.10 No protein-ligand interaction detected (PLIP)

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 5 residues within 4Å: Chain B: K.82, N.139, H.143 Chain D: K.82, N.139 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Salt bridges: B:K.82, B:H.143, B:H.146, D:K.82 Hydrogen bonds: D:N.139 PO4.5: 2 residues within 4Å: Chain B: H.143, K.144 4 PLIP interactions: 4 interactions with chain B Water bridges: B:K.144, B:K.144 Salt bridges: B:H.143, B:K.144 PO4.9: 2 residues within 4Å: Chain D: H.143, K.144 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:H.2 Salt bridges: D:H.143, D:K.144

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jenkins, J. et al., A triply ligated crystal structure of relaxed state human hemoglobin. TO BE PUBLISHED

Release Date

2008-06-03

Peptides

Hemoglobin subunit alpha: AC
Hemoglobin subunit beta: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Hemoglobin subunit alpha

Hemoglobin subunit beta

Related Entries With Identical Sequence