SMTL ID : 2zs0.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-6-6-6-6-mer

Ligands

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

HEM.1: 23 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.138 Chain D: H.91, Q.95 Ligands: OXY.2, GOL.15 22 PLIP interactions: 20 interactions with chain A, 2 interactions with chain D, Hydrophobic interactions: A:L.45, 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.138 Hydrogen bonds: A:Q.93, D:Q.95 Water bridges: A:H.62, A:R.97, A:R.97 Salt bridges: A:R.97, D:H.91 pi-Stacking: A:H.62 Metal complexes: A:H.94 HEM.5: 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.6 22 PLIP interactions: 20 interactions with chain B, 2 interactions with chain C, Hydrophobic interactions: B:L.45, B:F.46, B:F.46, B:V.66, B:I.99, B:I.99, B:Y.104, B:Y.104, B:F.107, B:F.107, B:I.136, B:V.137, B:I.140 Water bridges: B:V.49, B:R.65 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.9: 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.10 26 PLIP interactions: 19 interactions with chain C, 7 interactions with chain B, Hydrophobic interactions: C:F.50, C:F.50, C:F.50, C:L.94, C:H.108, C:F.109, C:F.109, C:F.109, C:M.112, C:F.136, C:I.143 Water bridges: C:V.53, C:Q.97, C:R.101, B:R.89, B:R.89, B:Q.93, 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 pi-Cation interactions: C:H.98 Metal complexes: C:H.98 HEM.13: 22 residues within 4Å: Chain A: H.89, Q.93 Chain D: F.39, M.49, F.50, P.51, Q.64, R.67, V.68, 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 20 PLIP interactions: 15 interactions with chain D, 5 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.102, D:V.107, D:L.110, D:L.110, D:I.141 Hydrogen bonds: D:R.67, D:Q.95, A:Q.93 Metal complexes: D:H.96 Water bridges: A:H.89, A:H.89 Salt bridges: A:H.89, A:H.89 HEM.16: 23 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.138 Chain H: H.91, Q.95 Ligands: OXY.17, GOL.30 22 PLIP interactions: 2 interactions with chain H, 20 interactions with chain E, Hydrogen bonds: H:Q.95, E:Q.93 Salt bridges: H:H.91, E:R.97 Hydrophobic interactions: E:L.45, 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.138 Water bridges: E:H.62, E:R.97, E:R.97 pi-Stacking: E:H.62 Metal complexes: E:H.94 HEM.20: 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.21 22 PLIP interactions: 2 interactions with chain G, 20 interactions with chain F, Hydrogen bonds: G:Q.97 Salt bridges: G:H.93, F:R.48, F:R.97 Hydrophobic interactions: F:L.45, F:F.46, F:F.46, F:V.66, F:I.99, F:I.99, F:Y.104, F:Y.104, F:F.107, F:F.107, F:I.136, F:V.137, F:I.140 Water bridges: F:V.49, F:R.65 pi-Stacking: F:H.62 pi-Cation interactions: F:H.94 Metal complexes: F:H.94 HEM.24: 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.25 26 PLIP interactions: 19 interactions with chain G, 7 interactions with chain F, Hydrophobic interactions: G:F.50, G:F.50, G:F.50, G:L.94, G:H.108, G:F.109, G:F.109, G:F.109, G:M.112, G:F.136, G:I.143 Water bridges: G:V.53, G:Q.97, G:R.101, F:R.89, F:R.89, F:Q.93, 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 pi-Cation interactions: G:H.98 Metal complexes: G:H.98 HEM.28: 22 residues within 4Å: Chain E: H.89, Q.93 Chain H: F.39, M.49, F.50, P.51, Q.64, R.67, V.68, 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.29 20 PLIP interactions: 15 interactions with chain H, 5 interactions with chain E, 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.102, H:V.107, H:L.110, H:L.110, H:I.141 Hydrogen bonds: H:R.67, H:Q.95, E:Q.93 Metal complexes: H:H.96 Water bridges: E:H.89, E:H.89 Salt bridges: E:H.89, E:H.89 HEM.31: 23 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.138 Chain L: H.91, Q.95 Ligands: OXY.32, GOL.45 22 PLIP interactions: 20 interactions with chain I, 2 interactions with chain L, Hydrophobic interactions: I:L.45, 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.138 Hydrogen bonds: I:Q.93, L:Q.95 Water bridges: I:H.62, I:R.97, I:R.97 Salt bridges: I:R.97, L:H.91 pi-Stacking: I:H.62 Metal complexes: I:H.94 HEM.35: 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.36 22 PLIP interactions: 20 interactions with chain J, 2 interactions with chain K, Hydrophobic interactions: J:L.45, J:F.46, J:F.46, J:V.66, J:I.99, J:I.99, J:Y.104, J:Y.104, J:F.107, J:F.107, J:I.136, J:V.137, J:I.140 Water bridges: J:V.49, J:R.65 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.39: 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.40 26 PLIP interactions: 19 interactions with chain K, 7 interactions with chain J, Hydrophobic interactions: K:F.50, K:F.50, K:F.50, K:L.94, K:H.108, K:F.109, K:F.109, K:F.109, K:M.112, K:F.136, K:I.143 Water bridges: K:V.53, K:Q.97, K:R.101, J:R.89, J:R.89, J:Q.93, 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 pi-Cation interactions: K:H.98 Metal complexes: K:H.98 HEM.43: 22 residues within 4Å: Chain I: H.89, Q.93 Chain L: F.39, M.49, F.50, P.51, Q.64, R.67, V.68, 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.44 20 PLIP interactions: 15 interactions with chain L, 5 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.102, L:V.107, L:L.110, L:L.110, L:I.141 Hydrogen bonds: L:R.67, L:Q.95, I:Q.93 Metal complexes: L:H.96 Water bridges: I:H.89, I:H.89 Salt bridges: I:H.89, I:H.89 HEM.46: 23 residues within 4Å: Chain M: 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.138 Chain P: H.91, Q.95 Ligands: OXY.47, GOL.60 21 PLIP interactions: 19 interactions with chain M, 2 interactions with chain P, Hydrophobic interactions: M:L.45, M:F.46, M:V.49, M:L.70, M:L.90, M:R.97, M:L.99, M:L.99, M:N.103, M:F.104, M:M.107, M:Y.131, M:I.138 Hydrogen bonds: M:Q.93, P:Q.95 Water bridges: M:R.97, M:R.97 Salt bridges: M:R.97, P:H.91 pi-Stacking: M:H.62 Metal complexes: M:H.94 HEM.50: 23 residues within 4Å: Chain N: 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 O: H.93, Q.97 Ligands: OXY.51 22 PLIP interactions: 20 interactions with chain N, 2 interactions with chain O, Hydrophobic interactions: N:L.45, N:F.46, N:F.46, N:V.66, N:I.99, N:I.99, N:Y.104, N:Y.104, N:F.107, N:F.107, N:I.136, N:V.137, N:I.140 Water bridges: N:V.49, N:R.65 Salt bridges: N:R.48, N:R.97, O:H.93 pi-Stacking: N:H.62 pi-Cation interactions: N:H.94 Metal complexes: N:H.94 Hydrogen bonds: O:Q.97 HEM.54: 21 residues within 4Å: Chain N: R.89, Q.93 Chain O: 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.55 26 PLIP interactions: 19 interactions with chain O, 7 interactions with chain N, Hydrophobic interactions: O:F.50, O:F.50, O:F.50, O:L.94, O:H.108, O:F.109, O:F.109, O:F.109, O:M.112, O:F.136, O:I.143 Water bridges: O:V.53, O:Q.97, O:R.101, N:R.89, N:R.89, N:Q.93, N:Q.93, N:Q.93 Salt bridges: O:R.101, O:R.101, N:R.89, N:R.89 pi-Stacking: O:H.66 pi-Cation interactions: O:H.98 Metal complexes: O:H.98 HEM.58: 22 residues within 4Å: Chain M: H.89, Q.93 Chain P: F.39, M.49, F.50, P.51, Q.64, R.67, V.68, 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.59 18 PLIP interactions: 15 interactions with chain P, 3 interactions with chain M, Hydrophobic interactions: P:F.39, P:F.50, P:F.50, P:P.51, P:L.92, P:I.99, P:I.99, P:V.102, P:V.107, P:L.110, P:L.110, P:I.141 Hydrogen bonds: P:R.67, P:Q.95, M:Q.93 Metal complexes: P:H.96 Salt bridges: M:H.89, M:H.89 HEM.61: 23 residues within 4Å: Chain Q: 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.138 Chain T: H.91, Q.95 Ligands: OXY.62, GOL.75 21 PLIP interactions: 19 interactions with chain Q, 2 interactions with chain T, Hydrophobic interactions: Q:L.45, Q:F.46, Q:V.49, Q:L.70, Q:L.90, Q:R.97, Q:L.99, Q:L.99, Q:N.103, Q:F.104, Q:M.107, Q:Y.131, Q:I.138 Hydrogen bonds: Q:Q.93, T:Q.95 Water bridges: Q:R.97, Q:R.97 Salt bridges: Q:R.97, T:H.91 pi-Stacking: Q:H.62 Metal complexes: Q:H.94 HEM.65: 23 residues within 4Å: Chain R: 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 S: H.93, Q.97 Ligands: OXY.66 22 PLIP interactions: 2 interactions with chain S, 20 interactions with chain R, Hydrogen bonds: S:Q.97 Salt bridges: S:H.93, R:R.48, R:R.97 Hydrophobic interactions: R:L.45, R:F.46, R:F.46, R:V.66, R:I.99, R:I.99, R:Y.104, R:Y.104, R:F.107, R:F.107, R:I.136, R:V.137, R:I.140 Water bridges: R:V.49, R:R.65 pi-Stacking: R:H.62 pi-Cation interactions: R:H.94 Metal complexes: R:H.94 HEM.69: 21 residues within 4Å: Chain R: R.89, Q.93 Chain S: 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.70 26 PLIP interactions: 7 interactions with chain R, 19 interactions with chain S, Water bridges: R:R.89, R:R.89, R:Q.93, R:Q.93, R:Q.93, S:V.53, S:Q.97, S:R.101 Salt bridges: R:R.89, R:R.89, S:R.101, S:R.101 Hydrophobic interactions: S:F.50, S:F.50, S:F.50, S:L.94, S:H.108, S:F.109, S:F.109, S:F.109, S:M.112, S:F.136, S:I.143 pi-Stacking: S:H.66 pi-Cation interactions: S:H.98 Metal complexes: S:H.98 HEM.73: 22 residues within 4Å: Chain Q: H.89, Q.93 Chain T: F.39, M.49, F.50, P.51, Q.64, R.67, V.68, 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.74 18 PLIP interactions: 15 interactions with chain T, 3 interactions with chain Q, Hydrophobic interactions: T:F.39, T:F.50, T:F.50, T:P.51, T:L.92, T:I.99, T:I.99, T:V.102, T:V.107, T:L.110, T:L.110, T:I.141 Hydrogen bonds: T:R.67, T:Q.95, Q:Q.93 Metal complexes: T:H.96 Salt bridges: Q:H.89, Q:H.89 HEM.76: 23 residues within 4Å: Chain U: 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.138 Chain X: H.91, Q.95 Ligands: OXY.77, GOL.90 21 PLIP interactions: 19 interactions with chain U, 2 interactions with chain X, Hydrophobic interactions: U:L.45, U:F.46, U:V.49, U:L.70, U:L.90, U:R.97, U:L.99, U:L.99, U:N.103, U:F.104, U:M.107, U:Y.131, U:I.138 Hydrogen bonds: U:Q.93, X:Q.95 Water bridges: U:R.97, U:R.97 Salt bridges: U:R.97, X:H.91 pi-Stacking: U:H.62 Metal complexes: U:H.94 HEM.80: 23 residues within 4Å: Chain V: 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 W: H.93, Q.97 Ligands: OXY.81 22 PLIP interactions: 20 interactions with chain V, 2 interactions with chain W, Hydrophobic interactions: V:L.45, V:F.46, V:F.46, V:V.66, V:I.99, V:I.99, V:Y.104, V:Y.104, V:F.107, V:F.107, V:I.136, V:V.137, V:I.140 Water bridges: V:V.49, V:R.65 Salt bridges: V:R.48, V:R.97, W:H.93 pi-Stacking: V:H.62 pi-Cation interactions: V:H.94 Metal complexes: V:H.94 Hydrogen bonds: W:Q.97 HEM.84: 21 residues within 4Å: Chain V: R.89, Q.93 Chain W: 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.85 26 PLIP interactions: 19 interactions with chain W, 7 interactions with chain V, Hydrophobic interactions: W:F.50, W:F.50, W:F.50, W:L.94, W:H.108, W:F.109, W:F.109, W:F.109, W:M.112, W:F.136, W:I.143 Water bridges: W:V.53, W:Q.97, W:R.101, V:R.89, V:R.89, V:Q.93, V:Q.93, V:Q.93 Salt bridges: W:R.101, W:R.101, V:R.89, V:R.89 pi-Stacking: W:H.66 pi-Cation interactions: W:H.98 Metal complexes: W:H.98 HEM.88: 22 residues within 4Å: Chain U: H.89, Q.93 Chain X: F.39, M.49, F.50, P.51, Q.64, R.67, V.68, 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.89 18 PLIP interactions: 15 interactions with chain X, 3 interactions with chain U, Hydrophobic interactions: X:F.39, X:F.50, X:F.50, X:P.51, X:L.92, X:I.99, X:I.99, X:V.102, X:V.107, X:L.110, X:L.110, X:I.141 Hydrogen bonds: X:R.67, X:Q.95, U:Q.93 Metal complexes: X:H.96 Salt bridges: U:H.89, U:H.89

24 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.6: 6 residues within 4Å: Chain B: W.32, F.46, H.62, V.66, H.94 Ligands: HEM.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.62 OXY.10: 6 residues within 4Å: Chain C: F.36, F.50, H.66, V.70, H.98 Ligands: HEM.9 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.66 OXY.14: 6 residues within 4Å: Chain D: F.36, F.50, Q.64, V.68, H.96 Ligands: HEM.13 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.64 OXY.17: 7 residues within 4Å: Chain E: F.32, F.46, H.62, V.66, H.94, M.107 Ligands: HEM.16 No protein-ligand interaction detected (PLIP) OXY.21: 6 residues within 4Å: Chain F: W.32, F.46, H.62, V.66, H.94 Ligands: HEM.20 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:H.62 OXY.25: 6 residues within 4Å: Chain G: F.36, F.50, H.66, V.70, H.98 Ligands: HEM.24 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:H.66 OXY.29: 6 residues within 4Å: Chain H: F.36, F.50, Q.64, V.68, H.96 Ligands: HEM.28 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:Q.64 OXY.32: 7 residues within 4Å: Chain I: F.32, F.46, H.62, V.66, H.94, M.107 Ligands: HEM.31 No protein-ligand interaction detected (PLIP) OXY.36: 6 residues within 4Å: Chain J: W.32, F.46, H.62, V.66, H.94 Ligands: HEM.35 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:H.62 OXY.40: 6 residues within 4Å: Chain K: F.36, F.50, H.66, V.70, H.98 Ligands: HEM.39 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:H.66 OXY.44: 6 residues within 4Å: Chain L: F.36, F.50, Q.64, V.68, H.96 Ligands: HEM.43 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:Q.64 OXY.47: 7 residues within 4Å: Chain M: F.32, F.46, H.62, V.66, H.94, M.107 Ligands: HEM.46 No protein-ligand interaction detected (PLIP) OXY.51: 6 residues within 4Å: Chain N: W.32, F.46, H.62, V.66, H.94 Ligands: HEM.50 1 PLIP interactions: 1 interactions with chain N Hydrogen bonds: N:H.62 OXY.55: 6 residues within 4Å: Chain O: F.36, F.50, H.66, V.70, H.98 Ligands: HEM.54 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:H.66 OXY.59: 6 residues within 4Å: Chain P: F.36, F.50, Q.64, V.68, H.96 Ligands: HEM.58 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:Q.64 OXY.62: 7 residues within 4Å: Chain Q: F.32, F.46, H.62, V.66, H.94, M.107 Ligands: HEM.61 No protein-ligand interaction detected (PLIP) OXY.66: 6 residues within 4Å: Chain R: W.32, F.46, H.62, V.66, H.94 Ligands: HEM.65 1 PLIP interactions: 1 interactions with chain R Hydrogen bonds: R:H.62 OXY.70: 6 residues within 4Å: Chain S: F.36, F.50, H.66, V.70, H.98 Ligands: HEM.69 1 PLIP interactions: 1 interactions with chain S Hydrogen bonds: S:H.66 OXY.74: 6 residues within 4Å: Chain T: F.36, F.50, Q.64, V.68, H.96 Ligands: HEM.73 1 PLIP interactions: 1 interactions with chain T Hydrogen bonds: T:Q.64 OXY.77: 7 residues within 4Å: Chain U: F.32, F.46, H.62, V.66, H.94, M.107 Ligands: HEM.76 No protein-ligand interaction detected (PLIP) OXY.81: 6 residues within 4Å: Chain V: W.32, F.46, H.62, V.66, H.94 Ligands: HEM.80 1 PLIP interactions: 1 interactions with chain V Hydrogen bonds: V:H.62 OXY.85: 6 residues within 4Å: Chain W: F.36, F.50, H.66, V.70, H.98 Ligands: HEM.84 1 PLIP interactions: 1 interactions with chain W Hydrogen bonds: W:H.66 OXY.89: 6 residues within 4Å: Chain X: F.36, F.50, Q.64, V.68, H.96 Ligands: HEM.88 1 PLIP interactions: 1 interactions with chain X Hydrogen bonds: X:Q.64

24 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: T.117 Chain M: L.119, D.120 Ligands: CA.48 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain M, 3 Ligand-Water interactions Metal complexes: A:T.117, M:L.119, H2O.6, H2O.91, H2O.91 CA.7: 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.11, H2O.12, H2O.12, H2O.13 CA.8: 2 residues within 4Å: Chain B: S.92, D.95 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.92, H2O.9, H2O.10, H2O.12, H2O.13 CA.11: 2 residues within 4Å: Chain B: D.78 Chain C: D.26 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.78, H2O.12, H2O.12, H2O.15, H2O.19 CA.18: 4 residues within 4Å: Chain E: T.117 Chain U: L.119, D.120 Ligands: CA.78 5 PLIP interactions: 1 interactions with chain E, 1 interactions with chain U, 3 Ligand-Water interactions Metal complexes: E:T.117, U:L.119, H2O.34, H2O.149, H2O.149 CA.22: 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.39, H2O.40, H2O.40, H2O.42 CA.23: 2 residues within 4Å: Chain F: S.92, D.95 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:S.92, H2O.38, H2O.38, H2O.41, H2O.42 CA.26: 2 residues within 4Å: Chain F: D.78 Chain G: D.26 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:D.78, H2O.40, H2O.40, H2O.43, H2O.47 CA.33: 4 residues within 4Å: Chain I: T.117 Chain Q: L.119, D.120 Ligands: CA.63 5 PLIP interactions: 1 interactions with chain Q, 1 interactions with chain I, 3 Ligand-Water interactions Metal complexes: Q:L.119, I:T.117, H2O.63, H2O.120, H2O.120 CA.37: 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.68, H2O.69, H2O.69, H2O.70 CA.38: 2 residues within 4Å: Chain J: S.92, D.95 5 PLIP interactions: 1 interactions with chain J, 4 Ligand-Water interactions Metal complexes: J:S.92, H2O.66, H2O.67, H2O.69, H2O.70 CA.41: 2 residues within 4Å: Chain J: D.78 Chain K: D.26 5 PLIP interactions: 1 interactions with chain J, 4 Ligand-Water interactions Metal complexes: J:D.78, H2O.69, H2O.69, H2O.72, H2O.76 CA.48: 4 residues within 4Å: Chain A: L.119, D.120 Chain M: T.117 Ligands: CA.3 5 PLIP interactions: 1 interactions with chain M, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: M:T.117, A:L.119, H2O.6, H2O.6, H2O.91 CA.52: 3 residues within 4Å: Chain N: D.55, S.56, S.57 5 PLIP interactions: 1 interactions with chain N, 4 Ligand-Water interactions Metal complexes: N:D.55, H2O.96, H2O.97, H2O.98, H2O.99 CA.53: 2 residues within 4Å: Chain N: S.92, D.95 5 PLIP interactions: 1 interactions with chain N, 4 Ligand-Water interactions Metal complexes: N:S.92, H2O.95, H2O.95, H2O.98, H2O.99 CA.56: 2 residues within 4Å: Chain N: D.78 Chain O: D.26 5 PLIP interactions: 1 interactions with chain N, 4 Ligand-Water interactions Metal complexes: N:D.78, H2O.97, H2O.97, H2O.100, H2O.105 CA.63: 4 residues within 4Å: Chain I: L.119, D.120 Chain Q: T.117 Ligands: CA.33 5 PLIP interactions: 1 interactions with chain I, 1 interactions with chain Q, 3 Ligand-Water interactions Metal complexes: I:L.119, Q:T.117, H2O.63, H2O.63, H2O.120 CA.67: 3 residues within 4Å: Chain R: D.55, S.56, S.57 5 PLIP interactions: 1 interactions with chain R, 4 Ligand-Water interactions Metal complexes: R:D.55, H2O.125, H2O.126, H2O.126, H2O.128 CA.68: 2 residues within 4Å: Chain R: S.92, D.95 5 PLIP interactions: 1 interactions with chain R, 4 Ligand-Water interactions Metal complexes: R:S.92, H2O.124, H2O.124, H2O.126, H2O.127 CA.71: 2 residues within 4Å: Chain R: D.78 Chain S: D.26 5 PLIP interactions: 1 interactions with chain R, 4 Ligand-Water interactions Metal complexes: R:D.78, H2O.126, H2O.126, H2O.129, H2O.133 CA.78: 4 residues within 4Å: Chain E: L.119, D.120 Chain U: T.117 Ligands: CA.18 5 PLIP interactions: 1 interactions with chain U, 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: U:T.117, E:L.119, H2O.34, H2O.34, H2O.149 CA.82: 3 residues within 4Å: Chain V: D.55, S.56, S.57 5 PLIP interactions: 1 interactions with chain V, 4 Ligand-Water interactions Metal complexes: V:D.55, H2O.153, H2O.154, H2O.155, H2O.156 CA.83: 2 residues within 4Å: Chain V: S.92, D.95 5 PLIP interactions: 1 interactions with chain V, 4 Ligand-Water interactions Metal complexes: V:S.92, H2O.152, H2O.152, H2O.155, H2O.156 CA.86: 2 residues within 4Å: Chain V: D.78 Chain W: D.26 5 PLIP interactions: 1 interactions with chain V, 4 Ligand-Water interactions Metal complexes: V:D.78, H2O.155, H2O.155, H2O.158, H2O.162

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

CL.4: 4 residues within 4Å: Chain A: R.4, I.8, K.11 Chain C: R.27 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain E: R.4, I.8, K.11 Chain G: R.27 Ligand excluded by PLIP CL.34: 4 residues within 4Å: Chain I: R.4, I.8, K.11 Chain K: R.27 Ligand excluded by PLIP CL.49: 4 residues within 4Å: Chain M: R.4, I.8, K.11 Chain O: R.27 Ligand excluded by PLIP CL.64: 4 residues within 4Å: Chain Q: R.4, I.8, K.11 Chain S: R.27 Ligand excluded by PLIP CL.79: 4 residues within 4Å: Chain U: R.4, I.8, K.11 Chain W: R.27 Ligand excluded by PLIP

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 4 residues within 4Å: Chain C: D.110, A.113, A.137, N.141 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.110, C:N.141 Water bridges: C:A.137 GOL.15: 4 residues within 4Å: Chain A: G.48, V.49 Chain D: H.91 Ligands: HEM.1 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Water bridges: D:S.87, D:H.91, A:R.65, A:R.97 GOL.27: 4 residues within 4Å: Chain G: D.110, A.113, A.137, N.141 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:D.110, G:N.141 Water bridges: G:A.137 GOL.30: 4 residues within 4Å: Chain E: G.48, V.49 Chain H: H.91 Ligands: HEM.16 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain E Water bridges: H:S.87, H:H.91, E:R.65, E:R.97 GOL.42: 4 residues within 4Å: Chain K: D.110, A.113, A.137, N.141 3 PLIP interactions: 3 interactions with chain K Hydrogen bonds: K:D.110, K:N.141 Water bridges: K:A.137 GOL.45: 4 residues within 4Å: Chain I: G.48, V.49 Chain L: H.91 Ligands: HEM.31 4 PLIP interactions: 2 interactions with chain L, 2 interactions with chain I Water bridges: L:S.87, L:H.91, I:R.65, I:R.97 GOL.57: 4 residues within 4Å: Chain O: D.110, A.113, A.137, N.141 4 PLIP interactions: 4 interactions with chain O Hydrogen bonds: O:D.110, O:D.110, O:N.141 Water bridges: O:A.137 GOL.60: 4 residues within 4Å: Chain M: G.48, V.49 Chain P: H.91 Ligands: HEM.46 5 PLIP interactions: 3 interactions with chain P, 2 interactions with chain M Hydrogen bonds: P:H.91 Water bridges: P:S.87, P:H.91, M:R.65, M:R.97 GOL.72: 4 residues within 4Å: Chain S: D.110, A.113, A.137, N.141 4 PLIP interactions: 4 interactions with chain S Hydrogen bonds: S:D.110, S:D.110, S:N.141 Water bridges: S:A.137 GOL.75: 4 residues within 4Å: Chain Q: G.48, V.49 Chain T: H.91 Ligands: HEM.61 5 PLIP interactions: 2 interactions with chain Q, 3 interactions with chain T Water bridges: Q:R.65, Q:R.97, T:S.87, T:H.91 Hydrogen bonds: T:H.91 GOL.87: 4 residues within 4Å: Chain W: D.110, A.113, A.137, N.141 4 PLIP interactions: 4 interactions with chain W Hydrogen bonds: W:D.110, W:D.110, W:N.141 Water bridges: W:A.137 GOL.90: 4 residues within 4Å: Chain U: G.48, V.49 Chain X: H.91 Ligands: HEM.76 5 PLIP interactions: 2 interactions with chain U, 3 interactions with chain X Water bridges: U:R.65, U:R.97, X:S.87, X:H.91 Hydrogen bonds: X:H.91

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: AEIMQU
Extracellular giant hemoglobin major globin subunit A2: BFJNRV
Extracellular giant hemoglobin major globin subunit B2: CGKOSW
Extracellular giant hemoglobin major globin subunit B1: DHLPTX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
A

I
A

M
A

Q
A

U
A

B
B

F
B

J
B

N
B

R
B

V
B

C
C

G
C

K
C

O
C

S
C

W
C

D
D

H
D

L
D

P
D

T
D

X
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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