SMTL ID : 7yb8.1

Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with D-2-hydroxyglutarate and factor X-derived peptide (39mer-4Ser)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

hetero-1-1-mer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: S.126, N.129, D.130, F.160, P.191 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.129, A:D.130 GOL.2: 6 residues within 4Å: Chain A: A.171, D.287, E.288, N.289 Chain B: G.21, E.22 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.22, A:D.287 Water bridges: A:E.288

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 6 residues within 4Å: Chain A: H.350, R.359, D.392, H.396 Chain B: D.18 Ligands: 2HG.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.350, A:H.396, H2O.5

1 x 2HG: (2R)-2-hydroxypentanedioic acid(Non-covalent)

2HG.4: 19 residues within 4Å: Chain A: W.296, Q.298, S.339, M.341, V.347, H.350, R.359, H.361, I.373, W.382, F.390, D.392, H.396, V.398, R.406, I.408, I.410 Chain B: D.18 Ligands: MN.3 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.296 Hydrogen bonds: A:W.296, A:Q.298, A:S.339, B:D.18 Salt bridges: A:R.359, A:H.361, A:H.361, A:H.396, A:R.406 Water bridges: B:D.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakashima, Y. et al., Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with D-2-hydroxyglutarate and factor X-derived peptide (39mer-4Ser). To Be Published

Release Date

2023-07-05

Peptides

Aspartyl/asparaginyl beta-hydroxylase: A
Coagulation factor X: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Aspartyl/asparaginyl beta-hydroxylase

Coagulation factor X

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