SMTL ID : 5ziq.1 (3 other biounits)

Crystal structure of hexacoordinated heme protein from anhydrobiotic tardigrade at pH 4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

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

HEM.1: 18 residues within 4Å: Chain A: L.53, M.60, L.63, F.64, A.84, A.87, H.88, P.91, Y.92, V.112, Q.115, H.116, V.119, F.122, Y.126, F.127, M.130, I.165 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:L.53, A:L.63, A:F.64, A:F.64, A:A.87, A:Y.92, A:V.112, A:Q.115, A:V.119, A:F.122, A:Y.126, A:F.127, A:M.130, A:I.165 Water bridges: A:A.84 pi-Stacking: A:F.122 Metal complexes: A:H.88, A:H.116

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

SO4.2: 2 residues within 4Å: Chain A: T.24, R.26 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.24 Water bridges: A:R.26, A:R.26, A:D.27 Salt bridges: A:R.26 SO4.3: 2 residues within 4Å: Chain A: R.111, R.114 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.111, A:R.114 SO4.4: 3 residues within 4Å: Chain A: K.61, K.68, A.69 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.69 Water bridges: A:D.62 Salt bridges: A:K.61, A:K.68

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 6 residues within 4Å: Chain A: P.22, L.23, T.24, D.27, R.152, I.156 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.22, A:T.24

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, J. et al., Crystal structure of Kumaglobin: a hexacoordinated heme protein from an anhydrobiotic tardigrade, Ramazzottius varieornatus. FEBS J. (2019)

Release Date

2019-01-02

Peptides

Globin protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Globin protein

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