SMTL ID : 7ybc.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

hetero-1-1-mer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: H.350, R.359, D.392, H.396 Chain B: D.18 Ligands: IOW.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.350, A:H.396, H2O.2, H2O.12

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: K.91, L.120, F.121, P.122, N.123, D.124 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.91, A:N.123, A:N.123

1 x IOW: (2~{S})-2-methyl-2-oxidanyl-4-oxidanylidene-pentanedioic acid(Non-covalent)

IOW.3: 18 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 Ligands: MN.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:W.296 Hydrogen bonds: A:W.296, A:S.339, A:S.339, A:S.339, A:D.392 Water bridges: A:K.337, A:R.359, A:R.359, A:R.359 Salt bridges: A:R.359, A:H.361, A:H.361, A:H.396, A:R.406

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 (S)-4-hydroxy-4-methyl-2-oxoglutarate 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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