SMTL ID : 5vpu.1

Crystal Structure of 2,3-bisphosphoglycerate-independent phosphoglycerate mutase bound to 3-phosphoglycerate, from Acinetobacter baumannii

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: D.411, H.415, H.453, H.471 Ligands: 3PG.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Ligand interactions Metal complexes: A:D.411, A:H.415, A:H.471, 3PG.3, 3PG.3 MN.2: 6 residues within 4Å: Chain A: D.25, S.75, K.344, D.452, H.453 Ligands: 3PG.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.25, A:D.25, A:S.75, A:D.452, A:H.453

1 x 3PG: 3-PHOSPHOGLYCERIC ACID(Non-covalent)

3PG.3: 19 residues within 4Å: Chain A: D.25, N.74, S.75, V.135, H.136, R.165, D.166, R.198, R.204, R.270, R.273, K.344, H.347, D.411, H.415, H.453, H.471 Ligands: MN.1, MN.2 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:S.75, A:R.198, A:R.198 Water bridges: A:R.204, A:R.204 Salt bridges: A:H.136, A:R.165, A:R.198, A:R.204, A:R.204, A:R.270, A:R.270, A:R.273, A:K.344, A:H.347, A:H.415, A:H.415, A:H.453, A:H.471

7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 5 residues within 4Å: Chain A: R.165, R.210, R.273, E.343, M.412 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.273, A:R.273 EDO.5: 4 residues within 4Å: Chain A: K.257, Q.259, D.260, V.293 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.257, A:D.260, A:D.260 Water bridges: A:K.257 EDO.6: 5 residues within 4Å: Chain A: N.45, A.48, M.49, G.434, Y.437 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.45 Water bridges: A:Y.437 EDO.7: 5 residues within 4Å: Chain A: F.92, T.96, H.138, D.140, H.141 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.138 EDO.8: 2 residues within 4Å: Chain A: G.253, E.254 No protein-ligand interaction detected (PLIP) EDO.9: 3 residues within 4Å: Chain A: F.200, D.209, Q.213 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.209, A:D.209 Water bridges: A:Q.213, A:K.248, A:K.248 EDO.10: 3 residues within 4Å: Chain A: V.87, L.88, Y.89 No protein-ligand interaction detected (PLIP)

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

ACT.11: 6 residues within 4Å: Chain A: S.61, G.62, D.69, G.70, Q.71, T.473 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.70 Water bridges: A:E.63, A:E.63 ACT.12: 2 residues within 4Å: Chain A: D.35, F.419 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.35, A:D.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Delker, S.L. et al., Crystal Structure of 2,3-bisphosphoglycerate-independent phosphoglycerate mutase bound to 3-phosphoglycerate, from Acinetobacter baumannii. to be published

Release Date

2017-05-24

Peptides

2,3-bisphosphoglycerate-independent phosphoglycerate mutase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

2,3-bisphosphoglycerate-independent phosphoglycerate mutase