SMTL ID : 5kgn.1 (1 other biounit)

1.95A resolution structure of independent phosphoglycerate mutase from C. elegans in complex with a macrocyclic peptide inhibitor (2d)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-1-1-mer

Ligands

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

CL.1: 2 residues within 4Å: Chain A: R.79, N.318 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: H.129, R.159, D.160, R.192, R.198, R.266, R.269 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.160, A:R.192, A:R.192, A:R.198, A:R.198, A:R.269, A:R.269 Water bridges: A:R.266

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: I.32, L.33, A.35, T.37 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:I.32, A:L.33, A:T.37, H2O.5, H2O.10

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

MN.4: 4 residues within 4Å: Chain A: S.68, D.408, H.412, H.467 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.408, A:D.408, A:H.412, A:H.467, H2O.12

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 6 residues within 4Å: Chain A: D.19, S.68, K.341, D.408, D.449, H.450 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.19, A:D.19, A:S.68, A:D.449, A:H.450

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, H. et al., Macrocycle peptides delineate locked-open inhibition mechanism for microorganism phosphoglycerate mutases. Nat Commun (2017)

Release Date

2017-04-05

Peptides

2,3-bisphosphoglycerate-independent phosphoglycerate mutase: A
macrocyclic peptide inhibitor: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

2,3-bisphosphoglycerate-independent phosphoglycerate mutase

macrocyclic peptide inhibitor

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