SMTL ID : 6z1m.3 (2 other biounits)

Structure of an Ancestral glycosidase (family 1) bound to heme

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

monomer

Ligands

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

HEM.1: 18 residues within 4Å: Chain A: P.172, N.173, L.202, L.203, H.206, I.224, L.226, L.228, F.251, N.252, F.255, L.256, Y.264, R.345, I.346, K.349, Y.350 Ligands: EDO.4 25 PLIP interactions: 25 interactions with chain A, Hydrophobic interactions: A:P.172, A:P.172, A:N.173, A:L.203, A:I.224, A:L.226, A:L.226, A:L.228, A:L.228, A:F.251, A:F.255, A:F.255, A:F.255, A:F.255, A:L.256, A:Y.264, A:Y.264, A:I.346, A:K.349, A:Y.350, A:Y.350 Water bridges: A:Y.232 Salt bridges: A:R.345 pi-Stacking: A:Y.264 Metal complexes: A:Y.264

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 10 residues within 4Å: Chain A: Q.25, H.126, N.170, E.171, N.302, Y.304, E.358, W.404, E.411, W.412 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.25, A:Q.25, A:N.170, A:E.171, A:N.302 Water bridges: A:E.411, A:E.411 GOL.3: 4 residues within 4Å: Chain A: V.231, Y.304, T.305, F.420 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.304, A:G.360

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

EDO.4: 5 residues within 4Å: Chain A: L.292, A.294, S.295, L.296 Ligands: HEM.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.292, A:L.296

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gamiz-Arco, G. et al., Heme-binding enables allosteric modulation in an ancient TIM-barrel glycosidase. Nat Commun (2021)

Release Date

2020-07-22

Peptides

Ancestral reconstructed glycosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Ancestral reconstructed glycosidase

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