SMTL ID : 4lr8.1 (2 other biounits)

Phosphopentomutase S154A variant soaked with ribose 5-phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: T.107, D.308, H.313, H.361 Ligands: HSX.7 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.107, A:D.308, A:D.308, A:H.313, A:H.361 MN.2: 5 residues within 4Å: Chain A: D.35, T.107, D.349, H.350 Ligands: HSX.7 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.35, A:D.35, A:T.107, A:D.349, A:H.350 MN.3: 4 residues within 4Å: Chain A: F.48, G.49, D.50, H.356 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:G.49, A:D.50, A:H.356, H2O.6, H2O.7, H2O.10

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.4: 2 residues within 4Å: Chain A: Y.118, Y.406 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.101, A:K.101

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 2 residues within 4Å: Chain A: P.373, K.376 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.376 Hydrogen bonds: A:E.340 Salt bridges: A:K.376

2 x HSX: 5-O-phosphono-alpha-D-ribofuranose(Non-covalent)(Post Translational Modification)

HSX.6: 14 residues within 4Å: Chain A: A.152, S.153, G.154, Y.174, A.176, D.178, V.180, Q.182, R.215, I.217, R.219, R.230, R.234 Ligands: HSX.7 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:G.154, A:Y.174, A:D.178, A:Q.182, A:Q.182, A:R.215, A:R.215 Water bridges: A:R.219, A:R.230, A:R.234, A:R.234, A:R.234 Salt bridges: A:R.219, A:R.219, A:R.230, A:R.234 HSX.7: 12 residues within 4Å: Chain A: T.107, D.178, R.215, V.305, D.308, A.309, H.313, H.350, H.361 Ligands: MN.1, MN.2, HSX.6 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.215, A:D.236 Salt bridges: A:R.215, A:K.262, A:H.361

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Birmingham, W.R. et al., Bioretrosynthetic construction of a didanosine biosynthetic pathway. Nat.Chem.Biol. (2014)

Release Date

2013-07-31

Peptides

Phosphopentomutase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Phosphopentomutase

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