SMTL ID : 7x8k.1 (3 other biounits)

Arabidopsis GDP-D-mannose pyrophosphorylase (VTC1) structure (product-bound)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

monomer

Ligands

1 x GDD: GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE(Non-covalent)

GDD.1: 23 residues within 4Å: Chain A: L.8, V.9, G.10, A.54, E.82, P.85, L.86, G.87, P.91, N.111, S.112, D.113, Y.147, G.148, E.164, N.175, A.176, G.177, Y.179, E.197, W.219, D.221 Ligands: FLC.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:A.54, A:L.86, A:G.87, A:N.111, A:D.113, A:G.148, A:E.164, A:N.175, A:N.175, A:A.176, A:E.197 Salt bridges: A:E.82

1 x FLC: CITRATE ANION(Non-covalent)

FLC.2: 7 residues within 4Å: Chain A: G.10, G.11, G.13, T.14, R.15, K.25 Ligands: GDD.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.11, A:R.15 Salt bridges: A:R.15, A:K.25, A:K.25

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 2 residues within 4Å: Chain A: T.230, R.233 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.230 Salt bridges: A:R.233 SO4.4: 4 residues within 4Å: Chain A: S.307, S.308, E.324, N.325 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.308, A:S.308, A:E.324, A:N.325 SO4.5: 2 residues within 4Å: Chain A: S.336, D.337 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.337, A:D.337 SO4.6: 2 residues within 4Å: Chain A: R.233, L.234 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.233 SO4.7: 2 residues within 4Å: Chain A: R.240, K.241 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.240 SO4.8: 4 residues within 4Å: Chain A: E.351, I.352, K.353, S.354 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.351, A:K.353, A:S.354

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, C. et al., Crystal Structures of Arabidopsis thaliana GDP-D-Mannose Pyrophosphorylase VITAMIN C DEFECTIVE 1. Front Plant Sci (2022)

Release Date

2022-05-18

Peptides

Mannose-1-phosphate guanylyltransferase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Mannose-1-phosphate guanylyltransferase 1

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