SMTL ID : 8re8.1

Aspartyl/Asparaginyl beta-hydroxylase (AspH) R688Q variant in complex with Mn, (3R)-methyl-2-oxoglutarate and a Factor X derived peptide fragment

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

hetero-1-1-mer

Ligands

1 x Q1Z: (3~{R})-3-methyl-2-oxidanylidene-pentanedioic acid(Non-covalent)

Q1Z.1: 16 residues within 4Å: Chain A: W.311, S.354, M.356, V.362, H.365, Q.374, H.376, W.397, F.405, H.411, V.413, R.421, I.423, I.425 Chain B: D.18 Ligands: MN.7 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.311, A:V.362, A:V.413, A:I.425 Hydrogen bonds: A:S.354, A:S.354, A:Q.374, A:D.407 Salt bridges: A:H.376, A:H.376, A:H.411, A:R.421

5 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 3 residues within 4Å: Chain A: K.387, T.394, W.414 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.387 PEG.3: 5 residues within 4Å: Chain A: K.106, F.136, P.137, N.138, D.139 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.106, A:K.106, A:N.138, A:N.138 PEG.4: 3 residues within 4Å: Chain A: W.246, N.392, F.409 No protein-ligand interaction detected (PLIP) PEG.5: 4 residues within 4Å: Chain A: R.306, E.307, K.308, G.309 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.309 Water bridges: A:G.309 PEG.6: 3 residues within 4Å: Chain A: R.284, L.288, V.380 No protein-ligand interaction detected (PLIP)

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

MN.7: 4 residues within 4Å: Chain A: H.365, H.411 Chain B: D.18 Ligands: Q1Z.1 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:H.365, A:H.411, B:D.18, H2O.12

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 3 residues within 4Å: Chain A: Y.57, P.58, Q.59 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brasnett, A. et al., Aspartyl/Asparaginyl beta-hydroxylase (AspH) R688Q variant in complex with Mn, (3R)-methyl-2-oxoglutarate and a Factor X derived peptide fragment. To Be Published

Release Date

2024-12-18

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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