SMTL ID : 1jw8.3 (2 other biounits)

1.3 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF P6 FORM OF MYOGLOBIN

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-hexamer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: T.52, E.53, A.54 Ligand excluded by PLIP SO4.2: 2 residues within 4Å: Chain A: A.16, K.17 Ligand excluded by PLIP SO4.3: 3 residues within 4Å: Chain A: G.125, A.126, D.127 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain B: T.52, E.53, A.54 Ligand excluded by PLIP SO4.7: 2 residues within 4Å: Chain B: A.16, K.17 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain B: G.125, A.126, D.127 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain C: T.52, E.53, A.54 Ligand excluded by PLIP SO4.12: 2 residues within 4Å: Chain C: A.16, K.17 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain C: G.125, A.126, D.127 Ligand excluded by PLIP SO4.16: 3 residues within 4Å: Chain D: T.52, E.53, A.54 Ligand excluded by PLIP SO4.17: 2 residues within 4Å: Chain D: A.16, K.17 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain D: G.125, A.126, D.127 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain E: T.52, E.53, A.54 Ligand excluded by PLIP SO4.22: 2 residues within 4Å: Chain E: A.16, K.17 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain E: G.125, A.126, D.127 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain F: T.52, E.53, A.54 Ligand excluded by PLIP SO4.27: 2 residues within 4Å: Chain F: A.16, K.17 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain F: G.125, A.126, D.127 Ligand excluded by PLIP

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

HEM.4: 18 residues within 4Å: Chain A: T.40, K.43, F.44, R.46, H.65, T.68, V.69, A.72, L.90, S.93, H.94, H.98, I.100, Y.104, L.105, I.108, F.139 Ligands: CMO.5 27 PLIP interactions: 26 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:F.44, A:F.44, A:F.44, A:T.68, A:V.69, A:V.69, A:A.72, A:L.90, A:L.90, A:I.100, A:Y.104, A:I.108, A:F.139, A:F.139 Hydrogen bonds: A:S.93 Water bridges: A:R.46, A:H.65, A:P.89, A:S.93 Salt bridges: A:R.46, A:H.65, A:H.94, A:H.98 pi-Stacking: A:H.94, A:H.98 Metal complexes: A:H.94, CMO.5 HEM.9: 18 residues within 4Å: Chain B: T.40, K.43, F.44, R.46, H.65, T.68, V.69, A.72, L.90, S.93, H.94, H.98, I.100, Y.104, L.105, I.108, F.139 Ligands: CMO.10 27 PLIP interactions: 26 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:F.44, B:F.44, B:F.44, B:T.68, B:V.69, B:V.69, B:A.72, B:L.90, B:L.90, B:I.100, B:Y.104, B:I.108, B:F.139, B:F.139 Hydrogen bonds: B:S.93 Water bridges: B:R.46, B:H.65, B:P.89, B:S.93 Salt bridges: B:R.46, B:H.65, B:H.94, B:H.98 pi-Stacking: B:H.94, B:H.98 Metal complexes: B:H.94, CMO.10 HEM.14: 18 residues within 4Å: Chain C: T.40, K.43, F.44, R.46, H.65, T.68, V.69, A.72, L.90, S.93, H.94, H.98, I.100, Y.104, L.105, I.108, F.139 Ligands: CMO.15 27 PLIP interactions: 26 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: C:F.44, C:F.44, C:F.44, C:T.68, C:V.69, C:V.69, C:A.72, C:L.90, C:L.90, C:I.100, C:Y.104, C:I.108, C:F.139, C:F.139 Hydrogen bonds: C:S.93 Water bridges: C:R.46, C:H.65, C:P.89, C:S.93 Salt bridges: C:R.46, C:H.65, C:H.94, C:H.98 pi-Stacking: C:H.94, C:H.98 Metal complexes: C:H.94, CMO.15 HEM.19: 18 residues within 4Å: Chain D: T.40, K.43, F.44, R.46, H.65, T.68, V.69, A.72, L.90, S.93, H.94, H.98, I.100, Y.104, L.105, I.108, F.139 Ligands: CMO.20 27 PLIP interactions: 26 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:F.44, D:F.44, D:F.44, D:T.68, D:V.69, D:V.69, D:A.72, D:L.90, D:L.90, D:I.100, D:Y.104, D:I.108, D:F.139, D:F.139 Hydrogen bonds: D:S.93 Water bridges: D:R.46, D:H.65, D:P.89, D:S.93 Salt bridges: D:R.46, D:H.65, D:H.94, D:H.98 pi-Stacking: D:H.94, D:H.98 Metal complexes: D:H.94, CMO.20 HEM.24: 18 residues within 4Å: Chain E: T.40, K.43, F.44, R.46, H.65, T.68, V.69, A.72, L.90, S.93, H.94, H.98, I.100, Y.104, L.105, I.108, F.139 Ligands: CMO.25 27 PLIP interactions: 26 interactions with chain E, 1 Ligand-Ligand interactions Hydrophobic interactions: E:F.44, E:F.44, E:F.44, E:T.68, E:V.69, E:V.69, E:A.72, E:L.90, E:L.90, E:I.100, E:Y.104, E:I.108, E:F.139, E:F.139 Hydrogen bonds: E:S.93 Water bridges: E:R.46, E:H.65, E:P.89, E:S.93 Salt bridges: E:R.46, E:H.65, E:H.94, E:H.98 pi-Stacking: E:H.94, E:H.98 Metal complexes: E:H.94, CMO.25 HEM.29: 18 residues within 4Å: Chain F: T.40, K.43, F.44, R.46, H.65, T.68, V.69, A.72, L.90, S.93, H.94, H.98, I.100, Y.104, L.105, I.108, F.139 Ligands: CMO.30 27 PLIP interactions: 26 interactions with chain F, 1 Ligand-Ligand interactions Hydrophobic interactions: F:F.44, F:F.44, F:F.44, F:T.68, F:V.69, F:V.69, F:A.72, F:L.90, F:L.90, F:I.100, F:Y.104, F:I.108, F:F.139, F:F.139 Hydrogen bonds: F:S.93 Water bridges: F:R.46, F:H.65, F:P.89, F:S.93 Salt bridges: F:R.46, F:H.65, F:H.94, F:H.98 pi-Stacking: F:H.94, F:H.98 Metal complexes: F:H.94, CMO.30

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

CMO.5: 5 residues within 4Å: Chain A: F.44, H.65, V.69, H.94 Ligands: HEM.4 No protein-ligand interaction detected (PLIP) CMO.10: 5 residues within 4Å: Chain B: F.44, H.65, V.69, H.94 Ligands: HEM.9 No protein-ligand interaction detected (PLIP) CMO.15: 5 residues within 4Å: Chain C: F.44, H.65, V.69, H.94 Ligands: HEM.14 No protein-ligand interaction detected (PLIP) CMO.20: 5 residues within 4Å: Chain D: F.44, H.65, V.69, H.94 Ligands: HEM.19 No protein-ligand interaction detected (PLIP) CMO.25: 5 residues within 4Å: Chain E: F.44, H.65, V.69, H.94 Ligands: HEM.24 No protein-ligand interaction detected (PLIP) CMO.30: 5 residues within 4Å: Chain F: F.44, H.65, V.69, H.94 Ligands: HEM.29 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kondrashov, D.A. et al., Sampling of the native conformational ensemble of myoglobin via structures in different crystalline environments. Proteins (2008)

Release Date

2001-10-10

Peptides

MYOGLOBIN: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

MYOGLOBIN

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