SMTL ID : 2w6y.1

Crystal structure of Sperm Whale Myoglobin mutant YQR in complex with Xenon

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 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, F.47, Q.65, R.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.5 21 PLIP interactions: 20 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:F.44, A:F.44, A:F.44, A:V.69, A:V.69, A:A.72, A:L.90, A:I.100, A:Y.104, A:I.108, A:I.108, A:F.139 Hydrogen bonds: A:S.93 Water bridges: A:Q.65, A:P.89 Salt bridges: A:R.46, A:H.94, A:H.98 pi-Stacking: A:H.98 Metal complexes: A:H.94, H2O.3

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

SO4.2: 2 residues within 4Å: Chain A: A.16, K.17 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.17 SO4.3: 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 SO4.4: 2 residues within 4Å: Chain A: S.4, E.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.5 Water bridges: A:G.6, A:G.6

4 x XE: XENON(Non-covalent)

XE.5: 4 residues within 4Å: Chain A: L.105, S.109, F.139 Ligands: HEM.1 No protein-ligand interaction detected (PLIP) XE.6: 4 residues within 4Å: Chain A: G.26, I.29, Y.30, V.69 No protein-ligand interaction detected (PLIP) XE.7: 2 residues within 4Å: Chain A: H.94, F.139 No protein-ligand interaction detected (PLIP) XE.8: 4 residues within 4Å: Chain A: I.76, H.83, A.135, F.139 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miele, A.E. et al., When the Same Fold Does not Mean the Same Function: The Case of Xenon Cavities in Hemoglobin and Myoglobin. To be Published

Release Date

2009-12-22

Peptides

MYOGLOBIN: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

MYOGLOBIN