SMTL ID : 8sg0.1

Crystal Structure of GDP-manose 3,5 epimerase de Myrciaria dubia in complex with substrate, product and NAD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-dimer

Ligands

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 30 residues within 4Å: Chain A: G.67, G.69, G.70, F.71, I.72, D.91, W.92, K.93, V.110, D.111, L.112, R.113, L.131, A.132, A.133, D.134, M.135, I.155, A.174, S.175, S.176, Y.206, K.210, F.233, N.235, I.236, K.249, R.403 Ligands: GDD.4, GDC.5 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:F.233 Hydrogen bonds: A:G.69, A:F.71, A:I.72, A:W.92, A:D.111, A:L.112, A:R.113, A:L.131, A:A.133, A:Y.206, A:K.210, A:I.236, A:I.236, A:K.249 Water bridges: A:A.73, A:T.242, A:T.242, A:K.249, A:R.403 pi-Stacking: A:W.92, A:W.92, A:F.233 NAD.6: 29 residues within 4Å: Chain B: G.67, G.69, G.70, F.71, I.72, D.91, W.92, K.93, V.110, D.111, L.112, R.113, L.131, A.132, A.133, D.134, M.135, I.155, A.174, S.175, S.176, Y.206, K.210, F.233, N.235, I.236, K.249 Ligands: GDD.7, GDC.8 31 PLIP interactions: 31 interactions with chain B Hydrophobic interactions: B:F.233 Hydrogen bonds: B:G.67, B:F.71, B:I.72, B:W.92, B:K.93, B:K.93, B:D.111, B:D.111, B:L.112, B:R.113, B:L.131, B:A.133, B:Y.206, B:K.210, B:I.236, B:I.236, B:K.249 Water bridges: B:A.73, B:K.93, B:D.134, B:T.242, B:T.242, B:T.242, B:T.242, B:T.242, B:K.249 Salt bridges: B:K.93 pi-Stacking: B:W.92, B:W.92, B:F.233

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

SO4.2: 1 residues within 4Å: Chain A: H.327 5 PLIP interactions: 5 interactions with chain A Water bridges: A:H.327, A:H.328, A:H.328, A:H.328 Salt bridges: A:H.327 SO4.3: 4 residues within 4Å: Chain A: T.274, M.306, S.308, E.311 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.308, A:S.308 Water bridges: A:S.308

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

GDD.4: 28 residues within 4Å: Chain A: M.135, G.136, G.137, M.138, I.141, S.176, C.178, Y.206, F.233, H.234, N.235, E.248, K.249, A.250, A.253, F.254, K.257, M.267, W.268, Q.273, R.275, M.309, P.332, E.333, R.338, S.388 Ligands: NAD.1, GDC.5 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:G.136, A:M.138, A:S.176, A:N.235, A:N.235, A:E.248, A:A.250, A:W.268, A:Q.273, A:E.333, A:R.338, A:S.388, A:S.388 Water bridges: A:R.338 Salt bridges: A:R.275, A:R.338, A:R.338 pi-Stacking: A:F.254, A:W.268 GDD.7: 28 residues within 4Å: Chain B: M.135, G.136, G.137, M.138, I.141, S.176, C.178, Y.206, F.233, H.234, N.235, E.248, K.249, A.250, A.253, F.254, K.257, M.267, W.268, Q.273, R.275, M.309, P.332, E.333, R.338, S.388 Ligands: NAD.6, GDC.8 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:G.136, B:M.138, B:S.176, B:F.233, B:N.235, B:N.235, B:E.248, B:A.250, B:W.268, B:Q.273, B:E.333, B:R.338, B:S.388, B:S.388 Water bridges: B:E.248, B:R.275 Salt bridges: B:R.275, B:R.338, B:R.338 pi-Stacking: B:F.254, B:W.268, B:W.268

2 x GDC: GUANOSINE-5'-DIPHOSPHATE-BETA-L-GALACTOSE(Non-covalent)

GDC.5: 29 residues within 4Å: Chain A: M.135, G.136, G.137, M.138, I.141, S.176, A.177, C.178, Y.206, F.233, H.234, N.235, E.248, K.249, A.250, A.253, F.254, K.257, M.267, W.268, Q.273, R.275, M.309, P.332, E.333, R.338, S.388 Ligands: NAD.1, GDD.4 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:G.136, A:M.138, A:S.176, A:N.235, A:N.235, A:E.248, A:A.250, A:W.268, A:Q.273, A:P.332, A:R.338, A:S.388, A:S.388 Water bridges: A:G.139, A:R.338 Salt bridges: A:R.275, A:R.338 pi-Stacking: A:F.254, A:W.268 GDC.8: 29 residues within 4Å: Chain B: M.135, G.136, G.137, M.138, I.141, S.176, A.177, C.178, Y.206, F.233, H.234, N.235, E.248, K.249, A.250, A.253, F.254, K.257, M.267, W.268, Q.273, R.275, M.309, P.332, E.333, R.338, S.388 Ligands: NAD.6, GDD.7 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:G.136, B:M.138, B:S.176, B:F.233, B:N.235, B:N.235, B:E.248, B:A.250, B:W.268, B:Q.273, B:P.332, B:R.338, B:S.388, B:S.388 Water bridges: B:G.139, B:E.248, B:R.275 Salt bridges: B:R.275, B:R.338, B:R.338 pi-Stacking: B:F.254, B:W.268

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vargas, J.A. et al., Structural insights into the Smirnoff-Wheeler pathway for vitamin C production in the Amazon fruit Camu-Camu. J.Exp.Bot. (2024)

Release Date

2024-03-13

Peptides

GDP-mannose 3,5-epimerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

GDP-mannose 3,5-epimerase

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