SMTL ID : 2x65.1

Crystal structure of T. maritima GDP-mannose pyrophosphorylase in complex with mannose-1-phosphate.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x M1P: 1-O-phosphono-alpha-D-mannopyranose(Non-covalent)

M1P.1: 14 residues within 4Å: Chain A: H.110, Y.149, G.150, F.168, E.170, K.171, N.189, S.190, G.191, F.193, D.239, W.258, D.260 Ligands: MG.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:H.110, A:G.150, A:E.170, A:N.189, A:N.189, A:D.239 Salt bridges: A:K.171, A:K.171 M1P.8: 13 residues within 4Å: Chain B: H.110, Y.149, G.150, F.168, E.170, K.171, N.189, S.190, G.191, D.239, W.258, D.260 Ligands: MG.9 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:H.110, B:G.150, B:E.170, B:N.189, B:N.189, B:D.239, B:D.260 Water bridges: B:E.170, B:K.171 Salt bridges: B:K.171, B:K.171

2 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.2: 1 residues within 4Å: Ligands: M1P.1 5 PLIP interactions: 4 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: H2O.1, H2O.3, H2O.3, H2O.3, M1P.1 MG.9: 2 residues within 4Å: Chain B: H.110 Ligands: M1P.8 No protein-ligand interaction detected (PLIP)

2 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.3: 3 residues within 4Å: Chain A: F.31, W.39, R.111 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.39, A:W.39 Hydrogen bonds: A:R.111 MRD.4: 3 residues within 4Å: Chain A: P.113, T.115, K.116 No protein-ligand interaction detected (PLIP)

3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.5: 2 residues within 4Å: Chain A: T.274, E.275 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.275 Water bridges: A:Y.273, A:T.274, A:R.287 MPD.6: 3 residues within 4Å: Chain A: K.66, P.70, D.74 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.70 MPD.7: 3 residues within 4Å: Chain A: K.123, K.124, D.127 No protein-ligand interaction detected (PLIP)

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.10: 5 residues within 4Å: Chain B: S.11, G.12, E.13, R.14, R.326 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.13, B:E.13, B:R.14 Water bridges: B:R.14 Salt bridges: B:R.14, B:R.326

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pelissier, M.C. et al., Structural Insights Into the Catalytic Mechanism of Bacterial Guanosine-Diphospho-D-Mannose Pyrophosphorylase and its Regulation by Divalent Ions. J.Biol.Chem. (2010)

Release Date

2010-06-23

Peptides

MANNOSE-1-PHOSPHATE GUANYLYLTRANSFERASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

MANNOSE-1-PHOSPHATE GUANYLYLTRANSFERASE

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