SMTL ID : 4bl5.4 (5 other biounits)

Crystal structure of human GDP-L-fucose synthase with bound NADP and product GDP-L-fucose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 28 residues within 4Å: Chain A: G.29, G.30, S.31, G.32, L.33, V.34, S.57, S.58, A.61, D.62, L.63, L.84, A.85, A.86, V.88, M.108, C.127, L.128, S.129, Y.158, K.162, P.185, T.186, N.187, V.188, H.201, R.335 Ligands: GFB.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:P.185, A:V.188 Hydrogen bonds: A:G.29, A:S.31, A:S.31, A:S.31, A:G.32, A:L.33, A:V.34, A:S.58, A:D.62, A:L.63, A:L.84, A:A.86, A:Y.158, A:K.162, A:V.188, A:H.201 Salt bridges: A:R.335 NAP.3: 29 residues within 4Å: Chain B: G.29, G.30, S.31, G.32, L.33, V.34, S.57, S.58, A.61, D.62, L.63, T.64, L.84, A.85, A.86, V.88, M.108, C.127, L.128, S.129, Y.158, K.162, P.185, T.186, N.187, V.188, H.201, R.335 Ligands: GFB.4 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:P.185, B:V.188 Hydrogen bonds: B:G.29, B:S.31, B:S.31, B:S.31, B:G.32, B:L.33, B:V.34, B:S.58, B:S.58, B:S.58, B:K.59, B:D.62, B:D.62, B:L.63, B:L.84, B:A.86, B:Y.158, B:K.162, B:V.188 Salt bridges: B:R.335

2 x GFB: GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE(Non-covalent)

GFB.2: 25 residues within 4Å: Chain A: G.89, G.90, L.91, F.92, N.94, S.129, C.131, N.155, Y.158, N.187, G.200, H.201, V.202, L.206, K.209, V.222, W.223, G.224, P.228, R.230, I.267, S.291, D.292, K.297 Ligands: NAP.1 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:L.91, A:N.94, A:N.94, A:S.129, A:N.155, A:Y.158, A:N.187, A:G.200, A:V.202, A:W.223, A:S.291, A:D.292 Salt bridges: A:R.230, A:K.297, A:K.297 GFB.4: 25 residues within 4Å: Chain B: G.89, G.90, L.91, F.92, N.94, S.129, C.131, N.155, Y.158, N.187, G.200, H.201, V.202, L.206, K.209, V.222, W.223, G.224, P.228, R.230, I.267, S.291, D.292, K.297 Ligands: NAP.3 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:L.91, B:N.94, B:S.129, B:N.155, B:Y.158, B:N.187, B:G.200, B:H.201, B:V.202, B:W.223, B:S.291, B:D.292 Water bridges: B:G.90 Salt bridges: B:R.230, B:K.297, B:K.297

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vollmar, M. et al., Crystal Structure of Human Gdp-L-Fucose Synthase with Bound Nadp and Product Gdp-L-Fucose. To be Published

Release Date

2014-05-21

Peptides

GDP-L-FUCOSE SYNTHASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

GDP-L-FUCOSE SYNTHASE

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