SMTL ID : 2w6w.1

Crystal structure of recombinant Sperm Whale Myoglobin under 1atm of Xenon

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

monomer

Ligands

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

HEM.1: 19 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: XE.2, XE.3 22 PLIP interactions: 21 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:F.44, A:F.44, A:F.44, A:T.68, A:V.69, A:A.72, A:L.90, A:I.100, A:Y.104, A:L.105, A:I.108, A:I.108, A:I.108, A:F.139 Hydrogen bonds: A:S.93 Water bridges: A:R.46 Salt bridges: A:R.46, A:H.94, A:H.98 pi-Stacking: A:H.98 Metal complexes: A:H.94, H2O.4

4 x XE: XENON(Non-covalent)

XE.2: 4 residues within 4Å: Chain A: S.109, F.139, R.140 Ligands: HEM.1 No protein-ligand interaction detected (PLIP) XE.3: 2 residues within 4Å: Chain A: H.94 Ligands: HEM.1 No protein-ligand interaction detected (PLIP) XE.4: 5 residues within 4Å: Chain A: G.26, I.29, L.30, V.69, L.70 No protein-ligand interaction detected (PLIP) XE.5: 4 residues within 4Å: Chain A: I.76, H.83, A.135, F.139 No protein-ligand interaction detected (PLIP)

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

SO4.6: 3 residues within 4Å: Chain A: T.52, E.53, A.54 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.53, A:A.54 SO4.7: 3 residues within 4Å: Chain A: G.125, A.126, D.127 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.126, A:D.127, A:D.127 Water bridges: A:G.125, A:G.125, A:A.128 SO4.8: 3 residues within 4Å: Chain A: R.46, H.65, T.68 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.46 Salt bridges: A:R.46, A:H.65 SO4.9: 2 residues within 4Å: Chain A: A.16, K.17 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.17

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 3 residues within 4Å: Chain A: H.82, H.83, E.84 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.84 Water bridges: A:K.79, A:A.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Savino, C. et al., Pattern of Cavities in Globins: The Case of Human Hemoglobin. Biopolymers (2009)

Release Date

2009-04-28

Peptides

MYOGLOBIN: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

MYOGLOBIN

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