SMTL ID : 8rdi.1 (1 other biounit)

Crystal structure of UDP-galactose 4-epimerase from Pyrococcus horikoshii containing Y145F mutation and with bound NAD and GDP-L-fucose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 31 residues within 4Å: Chain A: G.7, A.9, G.10, F.11, I.12, D.31, D.32, L.33, S.34, A.35, G.36, G.55, D.56, M.57, R.58, L.76, A.77, A.78, P.80, T.118, S.119, S.120, F.145, K.149, L.172, A.173, N.174, I.175, N.181, H.182 Ligands: GFB.2 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:L.172 Hydrogen bonds: A:A.9, A:A.9, A:F.11, A:I.12, A:G.13, A:D.32, A:L.33, A:S.34, A:S.34, A:A.35, A:G.36, A:D.56, A:M.57, A:L.76, A:A.78, A:T.118, A:K.149, A:I.175, A:I.175 Salt bridges: A:H.182, A:H.182 NAD.3: 30 residues within 4Å: Chain B: G.7, A.9, G.10, F.11, I.12, G.13, D.31, D.32, L.33, S.34, A.35, G.36, G.55, D.56, M.57, R.58, L.76, A.77, A.78, P.80, T.118, S.119, F.145, K.149, L.172, A.173, N.174, I.175, H.182 Ligands: GFB.4 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:I.12, B:L.172, B:I.175 Hydrogen bonds: B:A.9, B:F.11, B:I.12, B:G.13, B:D.32, B:L.33, B:S.34, B:S.34, B:A.35, B:G.36, B:D.56, B:D.56, B:M.57, B:L.76, B:A.78, B:T.118, B:K.149, B:I.175, B:I.175 Salt bridges: B:H.182, B:H.182

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

GFB.2: 20 residues within 4Å: Chain A: P.80, S.120, S.121, T.122, F.145, N.174, H.182, G.183, V.184, D.187, F.188, L.202, Q.207, K.209, Y.211, V.248, G.276, W.277, D.280 Ligands: NAD.1 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:P.80, A:S.120, A:T.122, A:N.174, A:G.183, A:V.184, A:L.202, A:Q.207, A:G.276, A:D.280 Salt bridges: A:D.187, A:K.209, A:K.209, A:K.209 GFB.4: 23 residues within 4Å: Chain B: P.80, V.82, R.83, S.120, S.121, T.122, F.145, N.174, H.182, G.183, V.184, D.187, F.188, K.191, L.202, Q.207, K.209, Y.211, V.248, G.276, W.277, D.280 Ligands: NAD.3 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:P.80, B:S.120, B:N.174, B:V.184, B:L.202, B:Q.207, B:D.280 Salt bridges: B:D.187, B:K.209, B:K.209

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alvarez Quispe, C. et al., Structural, computational and biochemical analysis reveal new insights in the specificity of a promiscuous GDP-Gal4E. To Be Published

Release Date

2024-12-18

Peptides

SDR family NAD(P)-dependent oxidoreductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

SDR family NAD(P)-dependent oxidoreductase

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