SMTL ID : 5kd1.2 (1 other biounit)

Sperm whale myoglobin H64A with nitrosoamphetamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-trimer

Ligands

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

HEM.1: 18 residues within 4Å: Chain A: T.39, K.42, F.43, R.45, T.67, V.68, A.71, L.72, L.89, S.92, H.93, H.97, I.99, Y.103, L.104, I.107, F.138 Ligands: 3QM.6 23 PLIP interactions: 23 interactions with chain A, Hydrophobic interactions: A:F.43, A:F.43, A:F.43, A:T.67, A:V.68, A:L.89, A:L.89, A:H.97, A:I.99, A:Y.103, A:I.107, A:F.138, A:F.138 Hydrogen bonds: A:S.92 Water bridges: A:P.88, A:S.92 Salt bridges: A:R.45, A:H.93, A:H.97 pi-Stacking: A:H.93, A:H.93, A:H.97 Metal complexes: A:H.93 HEM.12: 18 residues within 4Å: Chain B: T.39, K.42, F.43, R.45, T.67, V.68, A.71, L.72, L.89, S.92, H.93, H.97, I.99, Y.103, L.104, I.107, F.138 Ligands: 3QM.17 23 PLIP interactions: 23 interactions with chain B, Hydrophobic interactions: B:F.43, B:F.43, B:F.43, B:T.67, B:V.68, B:L.89, B:L.89, B:H.97, B:I.99, B:Y.103, B:I.107, B:F.138, B:F.138 Hydrogen bonds: B:S.92 Water bridges: B:P.88, B:S.92 Salt bridges: B:R.45, B:H.93, B:H.97 pi-Stacking: B:H.93, B:H.93, B:H.97 Metal complexes: B:H.93 HEM.23: 18 residues within 4Å: Chain C: T.39, K.42, F.43, R.45, T.67, V.68, A.71, L.72, L.89, S.92, H.93, H.97, I.99, Y.103, L.104, I.107, F.138 Ligands: 3QM.28 23 PLIP interactions: 23 interactions with chain C, Hydrophobic interactions: C:F.43, C:F.43, C:F.43, C:T.67, C:V.68, C:L.89, C:L.89, C:H.97, C:I.99, C:Y.103, C:I.107, C:F.138, C:F.138 Hydrogen bonds: C:S.92 Water bridges: C:P.88, C:S.92 Salt bridges: C:R.45, C:H.93, C:H.97 pi-Stacking: C:H.93, C:H.93, C:H.97 Metal complexes: C:H.93

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: T.51, E.52, A.53 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.52, A:A.53 SO4.3: 8 residues within 4Å: Chain A: A.15, K.16 Chain B: A.15, K.16 Chain C: A.15, K.16 Ligands: SO4.14, SO4.25 9 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A, 3 interactions with chain C Water bridges: B:K.16, B:K.16, A:K.16, A:K.16, C:K.16, C:K.16 Salt bridges: B:K.16, A:K.16, C:K.16 SO4.4: 1 residues within 4Å: Chain A: K.87 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.87 SO4.5: 3 residues within 4Å: Chain A: S.3, G.5, E.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.3, A:S.3 Water bridges: A:G.5 SO4.13: 3 residues within 4Å: Chain B: T.51, E.52, A.53 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.52, B:A.53 SO4.14: 8 residues within 4Å: Chain A: A.15, K.16 Chain B: A.15, K.16 Chain C: A.15, K.16 Ligands: SO4.3, SO4.25 9 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A, 3 interactions with chain C Water bridges: B:K.16, B:K.16, A:K.16, A:K.16, C:K.16, C:K.16 Salt bridges: B:K.16, A:K.16, C:K.16 SO4.15: 1 residues within 4Å: Chain B: K.87 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.87 SO4.16: 3 residues within 4Å: Chain B: S.3, G.5, E.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.3, B:S.3 Water bridges: B:G.5 SO4.24: 3 residues within 4Å: Chain C: T.51, E.52, A.53 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.52, C:A.53 SO4.25: 8 residues within 4Å: Chain A: A.15, K.16 Chain B: A.15, K.16 Chain C: A.15, K.16 Ligands: SO4.3, SO4.14 9 PLIP interactions: 3 interactions with chain A, 3 interactions with chain C, 3 interactions with chain B Water bridges: A:K.16, A:K.16, C:K.16, C:K.16, B:K.16, B:K.16 Salt bridges: A:K.16, C:K.16, B:K.16 SO4.26: 1 residues within 4Å: Chain C: K.87 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:K.87 SO4.27: 3 residues within 4Å: Chain C: S.3, G.5, E.6 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.3, C:S.3 Water bridges: C:G.5

3 x 3QM: [(2R)-2-nitrosopropyl]benzene(Non-covalent)

3QM.6: 7 residues within 4Å: Chain A: L.29, F.43, A.64, T.67, V.68, I.107 Ligands: HEM.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.29, A:F.43, A:A.64, A:T.67, A:I.107 3QM.17: 7 residues within 4Å: Chain B: L.29, F.43, A.64, T.67, V.68, I.107 Ligands: HEM.12 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.29, B:F.43, B:A.64, B:T.67, B:I.107 3QM.28: 7 residues within 4Å: Chain C: L.29, F.43, A.64, T.67, V.68, I.107 Ligands: HEM.23 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.29, C:F.43, C:A.64, C:T.67, C:I.107

15 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: A.57, S.58, E.59, D.60 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.59, A:D.60 GOL.8: 2 residues within 4Å: Chain A: R.31, H.113 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.31, A:R.31, A:H.113 GOL.9: 8 residues within 4Å: Chain A: G.121, N.122, F.123, G.124, A.125, D.126, A.127 Chain B: K.77 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.124, A:D.126, A:A.127, B:K.77, B:K.77 GOL.10: 7 residues within 4Å: Chain A: K.78, H.81, H.82, E.83, A.84, E.85 Ligands: GOL.11 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.78, A:E.83, A:A.84, A:E.85 Water bridges: A:H.81 GOL.11: 2 residues within 4Å: Chain A: H.81 Ligands: GOL.10 No protein-ligand interaction detected (PLIP) GOL.18: 4 residues within 4Å: Chain B: A.57, S.58, E.59, D.60 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.59, B:D.60 GOL.19: 2 residues within 4Å: Chain B: R.31, H.113 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.31, B:R.31, B:H.113 GOL.20: 8 residues within 4Å: Chain B: G.121, N.122, F.123, G.124, A.125, D.126, A.127 Chain C: K.77 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:K.77, C:K.77, B:G.124, B:D.126, B:A.127 GOL.21: 7 residues within 4Å: Chain B: K.78, H.81, H.82, E.83, A.84, E.85 Ligands: GOL.22 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.78, B:E.83, B:A.84, B:E.85 Water bridges: B:H.81 GOL.22: 2 residues within 4Å: Chain B: H.81 Ligands: GOL.21 No protein-ligand interaction detected (PLIP) GOL.29: 4 residues within 4Å: Chain C: A.57, S.58, E.59, D.60 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.59, C:D.60 GOL.30: 2 residues within 4Å: Chain C: R.31, H.113 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.31, C:R.31, C:H.113 GOL.31: 8 residues within 4Å: Chain A: K.77 Chain C: G.121, N.122, F.123, G.124, A.125, D.126, A.127 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:G.124, C:D.126, C:A.127, A:K.77, A:K.77 GOL.32: 7 residues within 4Å: Chain C: K.78, H.81, H.82, E.83, A.84, E.85 Ligands: GOL.33 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.78, C:E.83, C:A.84, C:E.85 Water bridges: C:H.81 GOL.33: 2 residues within 4Å: Chain C: H.81 Ligands: GOL.32 No protein-ligand interaction detected (PLIP)

Links

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Citation

Wang, B. et al., Nitrosoamphetamine binding to myoglobin and hemoglobin: Crystal structure of the H64A myoglobin-nitrosoamphetamine adduct. Nitric Oxide (2017)

Release Date

2017-05-10

Peptides

Myoglobin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Myoglobin

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