SMTL ID : 5vwu.1

Crystal structure of oxidized Aspergillus fumigatus UDP-galactopyranose mutase complexed with NADH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-tetramer

Ligands

4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 32 residues within 4Å: Chain A: G.17, A.18, G.19, P.20, T.21, D.41, S.42, G.48, L.49, A.50, V.63, G.64, G.65, H.66, G.243, K.244, V.245, T.271, M.272, T.298, W.318, R.330, E.376, G.421, Y.422, G.449, R.450, G.459, N.460, Q.461, S.464 Ligands: NAI.2 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:L.49, A:T.298, A:Y.422 Hydrogen bonds: A:T.21, A:T.21, A:T.21, A:S.42, A:L.49, A:G.64, A:H.66, A:H.66, A:V.245, A:V.245, A:R.330, A:R.330, A:R.450, A:N.460, A:Q.461, A:Q.461, A:S.464 Water bridges: A:F.451 FAD.5: 31 residues within 4Å: Chain B: G.17, A.18, G.19, P.20, T.21, D.41, S.42, G.48, L.49, A.50, V.63, G.64, G.65, H.66, G.243, K.244, V.245, T.271, M.272, T.298, R.330, E.376, G.421, Y.422, G.449, R.450, G.459, N.460, Q.461, S.464 Ligands: NAI.6 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:L.49, B:T.298, B:Y.422 Hydrogen bonds: B:A.18, B:G.19, B:T.21, B:T.21, B:T.21, B:G.22, B:D.41, B:S.42, B:G.48, B:L.49, B:G.64, B:H.66, B:H.66, B:V.245, B:V.245, B:R.330, B:R.330, B:R.450, B:N.460, B:Q.461, B:Q.461, B:S.464 Water bridges: B:F.451 FAD.10: 28 residues within 4Å: Chain C: G.17, G.19, P.20, T.21, D.41, S.42, G.48, L.49, A.50, V.63, G.64, G.65, H.66, G.243, K.244, V.245, T.271, M.272, T.298, H.420, G.421, G.449, R.450, G.459, N.460, Q.461, S.464 Ligands: SO4.14 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:L.49, C:T.298 Hydrogen bonds: C:G.19, C:T.21, C:T.21, C:T.21, C:S.42, C:L.49, C:L.49, C:H.66, C:H.66, C:V.245, C:V.245, C:R.450, C:N.460, C:Q.461, C:Q.461, C:S.464 pi-Cation interactions: C:R.450 FAD.15: 28 residues within 4Å: Chain D: G.17, A.18, G.19, P.20, T.21, D.41, S.42, G.48, L.49, A.50, V.63, G.64, G.65, H.66, G.243, V.245, T.271, M.272, T.298, H.420, G.421, G.449, R.450, G.459, N.460, Q.461, S.464 Ligands: SO4.19 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:L.49, D:V.63, D:T.298 Hydrogen bonds: D:A.18, D:G.19, D:T.21, D:T.21, D:T.21, D:G.22, D:S.42, D:L.49, D:L.49, D:H.66, D:H.66, D:H.66, D:V.245, D:V.245, D:R.450, D:N.460, D:Q.461, D:Q.461, D:S.464

2 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.2: 16 residues within 4Å: Chain A: I.68, F.69, H.71, R.94, S.96, Y.107, Y.320, R.330, Y.422, R.450, Y.456, N.460, H.463, N.491 Ligands: FAD.1, SO4.4 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.456, A:N.460 Hydrogen bonds: A:R.94, A:S.96, A:S.96, A:Y.107, A:R.330, A:R.330, A:Y.422, A:R.450, A:R.450, A:Y.456, A:N.460 Salt bridges: A:H.71, A:H.71, A:H.463 pi-Stacking: A:Y.107 NAI.6: 15 residues within 4Å: Chain B: I.68, F.69, H.71, R.94, S.96, Y.107, Y.320, R.330, Y.422, R.450, Y.456, N.460, H.463 Ligands: FAD.5, SO4.9 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:Y.456, B:Y.456, B:N.460 Hydrogen bonds: B:R.94, B:S.96, B:S.96, B:Y.320, B:R.330, B:R.330, B:Y.422, B:Y.422, B:R.450, B:R.450, B:N.460 Salt bridges: B:H.71, B:H.71, B:H.463 pi-Stacking: B:Y.107

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

SO4.3: 4 residues within 4Å: Chain A: T.91, H.92, Q.93, K.316 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.93 Salt bridges: A:H.92, A:K.316 SO4.4: 4 residues within 4Å: Chain A: W.318, Y.320, R.330 Ligands: NAI.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.320 Salt bridges: A:R.330 SO4.7: 2 residues within 4Å: Chain B: K.73, R.499 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.499 SO4.8: 4 residues within 4Å: Chain B: T.91, H.92, Q.93, K.316 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.93 Salt bridges: B:H.92, B:K.316 SO4.9: 4 residues within 4Å: Chain B: W.318, Y.320, R.330 Ligands: NAI.6 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.330 SO4.11: 4 residues within 4Å: Chain C: P.310, E.311, R.312, K.405 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.312 Salt bridges: C:R.312 SO4.12: 2 residues within 4Å: Chain C: P.117, K.118 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.118 SO4.13: 4 residues within 4Å: Chain C: T.91, H.92, Q.93, I.95 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.93 Salt bridges: C:H.92 SO4.14: 6 residues within 4Å: Chain C: H.66, Y.422, R.450, Y.456, N.460 Ligands: FAD.10 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Y.422, C:Y.422, C:Y.456 Salt bridges: C:H.66, C:R.450 SO4.16: 2 residues within 4Å: Chain D: T.140, K.141 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.141 SO4.17: 4 residues within 4Å: Chain D: P.310, E.311, R.312, K.405 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.312 Salt bridges: D:R.312, D:K.405 SO4.18: 2 residues within 4Å: Chain D: P.117, K.118 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.118 SO4.19: 6 residues within 4Å: Chain D: H.66, Y.422, R.450, Y.456, N.460 Ligands: FAD.15 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.422 Salt bridges: D:H.66, D:R.450

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dhatwalia, R. et al., Identification of the NAD(P)H binding site of eukaryotic UDP-galactopyranose mutase. J. Am. Chem. Soc. (2012)

Release Date

2017-05-31

Peptides

UDP-galactopyranose mutase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

UDP-galactopyranose mutase

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