SMTL ID : 7spf.1

Crystal structure of sperm whale myoglobin variant sMb5(pCaaF)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.17 Å

Oligo State

monomer

Ligands

1 x NO3: NITRATE ION(Non-functional Binders)

NO3.1: 7 residues within 4Å: Chain A: L.10, N.123, F.124, G.125, A.126, C.127, A.128 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.125, A:C.127, A:A.128

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

HEM.2: 19 residues within 4Å: Chain A: T.40, K.43, F.44, R.46, V.65, T.68, A.69, A.72, L.73, L.90, S.93, H.94, H.98, I.100, Y.104, L.105, I.108, F.139 Ligands: OXY.3 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:F.44, A:F.44, A:F.44, A:T.68, A:A.69, A:A.72, A:L.73, A:L.90, A:L.90, A:I.100, A:Y.104, A:F.139, A:F.139 Hydrogen bonds: A:S.93 Water bridges: A:P.89 Salt bridges: A:R.46, A:H.94, A:H.98 pi-Stacking: A:H.98 Metal complexes: A:H.94

1 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.3: 4 residues within 4Å: Chain A: F.44, V.65, A.69 Ligands: HEM.2 No protein-ligand interaction detected (PLIP)

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

SO4.4: 3 residues within 4Å: Chain A: K.17, H.120, N.123 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.123 Salt bridges: A:H.120 SO4.5: 5 residues within 4Å: Chain A: E.19, A.20, D.21, V.22, A.23 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.21, A:V.22, A:A.23 SO4.6: 3 residues within 4Å: Chain A: K.35, T.52, E.53 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.53 Water bridges: A:A.54 Salt bridges: A:K.35 SO4.7: 2 residues within 4Å: Chain A: H.49, K.51 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.51 SO4.8: 1 residues within 4Å: Chain A: K.64 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.64, A:T.68 Salt bridges: A:K.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Iannuzzelli, J.A. et al., Tuning Enzyme Thermostability via Computationally Guided Covalent Stapling and Structural Basis of Enhanced Stabilization. Biochemistry (2022)

Release Date

2022-06-01

Peptides

Myoglobin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Myoglobin

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