SMTL ID : 6z1m.1 (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: 19 residues within 4Å: Chain A: P.172, N.173, A.199, L.202, L.203, H.206, I.224, L.226, L.228, F.251, N.252, F.255, L.256, K.261, Y.264, S.295, L.296, R.345, Y.350 23 PLIP interactions: 23 interactions with chain A, Hydrophobic interactions: A:P.172, A:P.172, A:N.173, A:A.199, A:L.202, A:L.203, A:I.224, A:L.228, A:F.251, A:F.255, A:F.255, A:F.255, A:Y.264, A:Y.264, A:Y.264, A:L.296, A:Y.350 Hydrogen bonds: A:Y.350, A:Y.350 Salt bridges: A:K.261, A:R.345 pi-Stacking: A:Y.264 Metal complexes: A:Y.264

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 11 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 Ligands: EDO.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.25, A:H.126, A:N.170, A:E.171, A:N.302, A:E.411 GOL.3: 3 residues within 4Å: Chain A: A.59, Y.416, Y.427 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.430 Water bridges: A:A.59, A:Y.416

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

EDO.4: 3 residues within 4Å: Chain A: R.214, G.220, D.297 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.297 EDO.5: 3 residues within 4Å: Chain A: Y.304, E.411 Ligands: GOL.2 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.171, A:N.227 EDO.6: 2 residues within 4Å: Chain A: D.364, K.418 2 PLIP interactions: 2 interactions with chain A Water bridges: A:V.363, A:V.363

1 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 2 residues within 4Å: Chain A: H.373, K.436 No protein-ligand interaction detected (PLIP)

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
A

Ancestral reconstructed glycosidase

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