SMTL ID : 2zs1.2 (1 other biounit)

Structural Basis for the Heterotropic and Homotropic Interactions of Invertebrate Giant Hemoglobin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-3-3-3-3-mer

Ligands

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

HEM.1: 24 residues within 4Å: Chain A: L.45, F.46, G.48, V.49, H.62, R.65, V.66, A.69, L.70, L.90, Q.93, H.94, R.97, L.99, N.103, F.104, M.107, Y.131, I.134, I.138 Chain D: H.91, Q.95 Ligands: OXY.2, GOL.3 25 PLIP interactions: 23 interactions with chain A, 2 interactions with chain D, Hydrophobic interactions: A:L.45, A:F.46, A:F.46, A:V.49, A:L.70, A:L.90, A:R.97, A:L.99, A:L.99, A:N.103, A:F.104, A:M.107, A:Y.131, A:I.134, A:I.138 Hydrogen bonds: A:Q.93, D:Q.95 Water bridges: A:R.65, A:R.97, A:R.97 Salt bridges: A:R.97, D:H.91 pi-Stacking: A:H.62 pi-Cation interactions: A:H.94 Metal complexes: A:H.94 HEM.8: 23 residues within 4Å: Chain B: L.45, F.46, R.48, V.49, H.62, R.65, V.66, G.69, L.70, L.90, Q.93, H.94, R.97, I.99, G.103, Y.104, F.107, I.136, V.137, I.140 Chain C: H.93, Q.97 Ligands: OXY.9 20 PLIP interactions: 18 interactions with chain B, 2 interactions with chain C, Hydrophobic interactions: B:L.45, B:F.46, B:F.46, B:I.99, B:I.99, B:Y.104, B:F.107, B:F.107, B:I.136, B:V.137, B:I.140 Water bridges: B:V.49, B:H.62 Salt bridges: B:R.48, B:R.97, C:H.93 pi-Stacking: B:H.62 pi-Cation interactions: B:H.94 Metal complexes: B:H.94 Hydrogen bonds: C:Q.97 HEM.11: 21 residues within 4Å: Chain B: R.89, Q.93 Chain C: L.49, F.50, G.52, V.53, H.66, R.69, V.70, L.74, L.94, Q.97, H.98, R.101, V.104, H.108, F.109, M.112, F.136, I.143 Ligands: OXY.12 28 PLIP interactions: 24 interactions with chain C, 4 interactions with chain B, Hydrophobic interactions: C:L.49, C:F.50, C:F.50, C:F.50, C:L.94, C:V.104, C:H.108, C:F.109, C:F.109, C:F.109, C:M.112, C:F.136, C:I.143 Water bridges: C:R.69, C:Q.97, C:R.101, C:R.101, C:R.101, B:Q.93, B:Q.93 Salt bridges: C:R.101, C:R.101, B:R.89, B:R.89 pi-Stacking: C:H.66, C:H.98, C:H.98 Metal complexes: C:H.98 HEM.13: 21 residues within 4Å: Chain A: H.89, Q.93 Chain D: F.39, M.49, F.50, P.51, Q.64, R.67, G.71, L.92, Q.95, H.96, I.99, G.101, V.102, A.106, V.107, L.110, S.111, I.141 Ligands: OXY.14 19 PLIP interactions: 15 interactions with chain D, 4 interactions with chain A, Hydrophobic interactions: D:F.39, D:F.50, D:F.50, D:P.51, D:L.92, D:I.99, D:I.99, D:V.107, D:L.110, D:L.110, D:I.141 Hydrogen bonds: D:Q.95, A:Q.93 Water bridges: D:R.67, A:H.89 pi-Cation interactions: D:H.96 Metal complexes: D:H.96 Salt bridges: A:H.89, A:H.89 HEM.17: 24 residues within 4Å: Chain E: L.45, F.46, G.48, V.49, H.62, R.65, V.66, A.69, L.70, L.90, Q.93, H.94, R.97, L.99, N.103, F.104, M.107, Y.131, I.134, I.138 Chain H: H.91, Q.95 Ligands: OXY.18, GOL.19 25 PLIP interactions: 23 interactions with chain E, 2 interactions with chain H, Hydrophobic interactions: E:L.45, E:F.46, E:F.46, E:V.49, E:L.70, E:L.90, E:R.97, E:L.99, E:L.99, E:N.103, E:F.104, E:M.107, E:Y.131, E:I.134, E:I.138 Hydrogen bonds: E:Q.93, H:Q.95 Water bridges: E:R.65, E:R.97, E:R.97 Salt bridges: E:R.97, H:H.91 pi-Stacking: E:H.62 pi-Cation interactions: E:H.94 Metal complexes: E:H.94 HEM.24: 23 residues within 4Å: Chain F: L.45, F.46, R.48, V.49, H.62, R.65, V.66, G.69, L.70, L.90, Q.93, H.94, R.97, I.99, G.103, Y.104, F.107, I.136, V.137, I.140 Chain G: H.93, Q.97 Ligands: OXY.25 20 PLIP interactions: 18 interactions with chain F, 2 interactions with chain G, Hydrophobic interactions: F:L.45, F:F.46, F:F.46, F:I.99, F:I.99, F:Y.104, F:F.107, F:F.107, F:I.136, F:V.137, F:I.140 Water bridges: F:V.49, F:H.62 Salt bridges: F:R.48, F:R.97, G:H.93 pi-Stacking: F:H.62 pi-Cation interactions: F:H.94 Metal complexes: F:H.94 Hydrogen bonds: G:Q.97 HEM.27: 21 residues within 4Å: Chain F: R.89, Q.93 Chain G: L.49, F.50, G.52, V.53, H.66, R.69, V.70, L.74, L.94, Q.97, H.98, R.101, V.104, H.108, F.109, M.112, F.136, I.143 Ligands: OXY.28 28 PLIP interactions: 24 interactions with chain G, 4 interactions with chain F, Hydrophobic interactions: G:L.49, G:F.50, G:F.50, G:F.50, G:L.94, G:V.104, G:H.108, G:F.109, G:F.109, G:F.109, G:M.112, G:F.136, G:I.143 Water bridges: G:R.69, G:Q.97, G:R.101, G:R.101, G:R.101, F:Q.93, F:Q.93 Salt bridges: G:R.101, G:R.101, F:R.89, F:R.89 pi-Stacking: G:H.66, G:H.98, G:H.98 Metal complexes: G:H.98 HEM.29: 21 residues within 4Å: Chain E: H.89, Q.93 Chain H: F.39, M.49, F.50, P.51, Q.64, R.67, G.71, L.92, Q.95, H.96, I.99, G.101, V.102, A.106, V.107, L.110, S.111, I.141 Ligands: OXY.30 19 PLIP interactions: 4 interactions with chain E, 15 interactions with chain H, Hydrogen bonds: E:Q.93, H:Q.95 Water bridges: E:H.89, H:R.67 Salt bridges: E:H.89, E:H.89 Hydrophobic interactions: H:F.39, H:F.50, H:F.50, H:P.51, H:L.92, H:I.99, H:I.99, H:V.107, H:L.110, H:L.110, H:I.141 pi-Cation interactions: H:H.96 Metal complexes: H:H.96 HEM.33: 24 residues within 4Å: Chain I: L.45, F.46, G.48, V.49, H.62, R.65, V.66, A.69, L.70, L.90, Q.93, H.94, R.97, L.99, N.103, F.104, M.107, Y.131, I.134, I.138 Chain L: H.91, Q.95 Ligands: OXY.34, GOL.35 25 PLIP interactions: 2 interactions with chain L, 23 interactions with chain I, Hydrogen bonds: L:Q.95, I:Q.93 Salt bridges: L:H.91, I:R.97 Hydrophobic interactions: I:L.45, I:F.46, I:F.46, I:V.49, I:L.70, I:L.90, I:R.97, I:L.99, I:L.99, I:N.103, I:F.104, I:M.107, I:Y.131, I:I.134, I:I.138 Water bridges: I:R.65, I:R.97, I:R.97 pi-Stacking: I:H.62 pi-Cation interactions: I:H.94 Metal complexes: I:H.94 HEM.40: 23 residues within 4Å: Chain J: L.45, F.46, R.48, V.49, H.62, R.65, V.66, G.69, L.70, L.90, Q.93, H.94, R.97, I.99, G.103, Y.104, F.107, I.136, V.137, I.140 Chain K: H.93, Q.97 Ligands: OXY.41 20 PLIP interactions: 18 interactions with chain J, 2 interactions with chain K, Hydrophobic interactions: J:L.45, J:F.46, J:F.46, J:I.99, J:I.99, J:Y.104, J:F.107, J:F.107, J:I.136, J:V.137, J:I.140 Water bridges: J:V.49, J:H.62 Salt bridges: J:R.48, J:R.97, K:H.93 pi-Stacking: J:H.62 pi-Cation interactions: J:H.94 Metal complexes: J:H.94 Hydrogen bonds: K:Q.97 HEM.43: 21 residues within 4Å: Chain J: R.89, Q.93 Chain K: L.49, F.50, G.52, V.53, H.66, R.69, V.70, L.74, L.94, Q.97, H.98, R.101, V.104, H.108, F.109, M.112, F.136, I.143 Ligands: OXY.44 28 PLIP interactions: 24 interactions with chain K, 4 interactions with chain J, Hydrophobic interactions: K:L.49, K:F.50, K:F.50, K:F.50, K:L.94, K:V.104, K:H.108, K:F.109, K:F.109, K:F.109, K:M.112, K:F.136, K:I.143 Water bridges: K:R.69, K:Q.97, K:R.101, K:R.101, K:R.101, J:Q.93, J:Q.93 Salt bridges: K:R.101, K:R.101, J:R.89, J:R.89 pi-Stacking: K:H.66, K:H.98, K:H.98 Metal complexes: K:H.98 HEM.45: 21 residues within 4Å: Chain I: H.89, Q.93 Chain L: F.39, M.49, F.50, P.51, Q.64, R.67, G.71, L.92, Q.95, H.96, I.99, G.101, V.102, A.106, V.107, L.110, S.111, I.141 Ligands: OXY.46 19 PLIP interactions: 15 interactions with chain L, 4 interactions with chain I, Hydrophobic interactions: L:F.39, L:F.50, L:F.50, L:P.51, L:L.92, L:I.99, L:I.99, L:V.107, L:L.110, L:L.110, L:I.141 Hydrogen bonds: L:Q.95, I:Q.93 Water bridges: L:R.67, I:H.89 pi-Cation interactions: L:H.96 Metal complexes: L:H.96 Salt bridges: I:H.89, I:H.89

12 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.2: 7 residues within 4Å: Chain A: F.32, F.46, H.62, V.66, H.94, M.107 Ligands: HEM.1 No protein-ligand interaction detected (PLIP) OXY.9: 6 residues within 4Å: Chain B: W.32, F.46, H.62, V.66, H.94 Ligands: HEM.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.62 OXY.12: 6 residues within 4Å: Chain C: F.36, F.50, H.66, V.70, H.98 Ligands: HEM.11 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.66 OXY.14: 7 residues within 4Å: Chain D: F.36, F.50, Q.64, V.68, H.96, L.110 Ligands: HEM.13 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.64 OXY.18: 7 residues within 4Å: Chain E: F.32, F.46, H.62, V.66, H.94, M.107 Ligands: HEM.17 No protein-ligand interaction detected (PLIP) OXY.25: 6 residues within 4Å: Chain F: W.32, F.46, H.62, V.66, H.94 Ligands: HEM.24 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:H.62 OXY.28: 6 residues within 4Å: Chain G: F.36, F.50, H.66, V.70, H.98 Ligands: HEM.27 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:H.66 OXY.30: 7 residues within 4Å: Chain H: F.36, F.50, Q.64, V.68, H.96, L.110 Ligands: HEM.29 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:Q.64 OXY.34: 7 residues within 4Å: Chain I: F.32, F.46, H.62, V.66, H.94, M.107 Ligands: HEM.33 No protein-ligand interaction detected (PLIP) OXY.41: 6 residues within 4Å: Chain J: W.32, F.46, H.62, V.66, H.94 Ligands: HEM.40 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:H.62 OXY.44: 6 residues within 4Å: Chain K: F.36, F.50, H.66, V.70, H.98 Ligands: HEM.43 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:H.66 OXY.46: 7 residues within 4Å: Chain L: F.36, F.50, Q.64, V.68, H.96, L.110 Ligands: HEM.45 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:Q.64

18 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: G.48, R.97 Chain D: H.91 Ligands: HEM.1 Ligand excluded by PLIP GOL.4: 5 residues within 4Å: Chain A: G.40, S.41, R.43, A.44, D.52 Ligand excluded by PLIP GOL.5: 5 residues within 4Å: Chain A: F.104, A.105, Y.131, E.132, A.135 Ligand excluded by PLIP GOL.6: 6 residues within 4Å: Chain A: Q.79, Q.80, A.81, T.82 Chain D: A.59, L.62 Ligand excluded by PLIP GOL.15: 4 residues within 4Å: Chain D: E.1, R.5, T.80, R.82 Ligand excluded by PLIP GOL.16: 7 residues within 4Å: Chain A: G.19, A.21, E.22, R.24 Chain D: I.12, D.16, N.77 Ligand excluded by PLIP GOL.19: 4 residues within 4Å: Chain E: G.48, R.97 Chain H: H.91 Ligands: HEM.17 Ligand excluded by PLIP GOL.20: 5 residues within 4Å: Chain E: G.40, S.41, R.43, A.44, D.52 Ligand excluded by PLIP GOL.21: 5 residues within 4Å: Chain E: F.104, A.105, Y.131, E.132, A.135 Ligand excluded by PLIP GOL.22: 6 residues within 4Å: Chain E: Q.79, Q.80, A.81, T.82 Chain H: A.59, L.62 Ligand excluded by PLIP GOL.31: 4 residues within 4Å: Chain H: E.1, R.5, T.80, R.82 Ligand excluded by PLIP GOL.32: 7 residues within 4Å: Chain E: G.19, A.21, E.22, R.24 Chain H: I.12, D.16, N.77 Ligand excluded by PLIP GOL.35: 4 residues within 4Å: Chain I: G.48, R.97 Chain L: H.91 Ligands: HEM.33 Ligand excluded by PLIP GOL.36: 5 residues within 4Å: Chain I: G.40, S.41, R.43, A.44, D.52 Ligand excluded by PLIP GOL.37: 5 residues within 4Å: Chain I: F.104, A.105, Y.131, E.132, A.135 Ligand excluded by PLIP GOL.38: 6 residues within 4Å: Chain I: Q.79, Q.80, A.81, T.82 Chain L: A.59, L.62 Ligand excluded by PLIP GOL.47: 4 residues within 4Å: Chain L: E.1, R.5, T.80, R.82 Ligand excluded by PLIP GOL.48: 7 residues within 4Å: Chain I: G.19, A.21, E.22, R.24 Chain L: I.12, D.16, N.77 Ligand excluded by PLIP

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 4 residues within 4Å: Chain A: R.4, I.8, K.11 Chain C: R.27 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain E: R.4, I.8, K.11 Chain G: R.27 Ligand excluded by PLIP CL.39: 4 residues within 4Å: Chain I: R.4, I.8, K.11 Chain K: R.27 Ligand excluded by PLIP

3 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 3 residues within 4Å: Chain B: D.55, S.56, S.57 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.55, H2O.10, H2O.11, H2O.11, H2O.35 MG.26: 3 residues within 4Å: Chain F: D.55, S.56, S.57 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:D.55, H2O.35, H2O.35, H2O.36, H2O.60 MG.42: 3 residues within 4Å: Chain J: D.55, S.56, S.57 5 PLIP interactions: 1 interactions with chain J, 4 Ligand-Water interactions Metal complexes: J:D.55, H2O.10, H2O.59, H2O.60, H2O.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Numoto, N. et al., Structural Basis for the Heterotropic and Homotropic Interactions of Invertebrate Giant Hemoglobin. Biochemistry (2008)

Release Date

2008-10-21

Peptides

Extracellular giant hemoglobin major globin subunit A1: AEI
Extracellular giant hemoglobin major globin subunit A2: BFJ
Extracellular giant hemoglobin major globin subunit B2: CGK
Extracellular giant hemoglobin major globin subunit B1: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
A

I
A

B
B

F
B

J
B

C
C

G
C

K
C

D
D

H
D

L
D

Extracellular giant hemoglobin major globin subunit A1

Extracellular giant hemoglobin major globin subunit A2

Extracellular giant hemoglobin major globin subunit B2

Extracellular giant hemoglobin major globin subunit B1

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