SMTL ID : 4wx1.1

Structure of Aspergillus fumigatus UDP-Galactopyranose mutase mutant F66A determined from a crystal soaked with UDP-Galactopyranose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x FDA: DIHYDROFLAVINE-ADENINE DINUCLEOTIDE(Non-covalent)

FDA.1: 30 residues within 4Å: Chain A: I.16, G.17, G.19, P.20, T.21, D.41, S.42, G.47, G.48, L.49, A.50, V.63, G.65, H.66, V.67, G.243, K.244, V.245, M.272, T.298, R.330, E.376, G.421, Y.422, G.449, R.450, G.459, N.460, Q.461, S.464 32 PLIP interactions: 32 interactions with chain A Hydrophobic interactions: A:V.63, A:T.298, A:Y.422 Hydrogen bonds: A:G.19, A:T.21, A:T.21, A:T.21, A:S.42, A:G.48, A:L.49, A:A.50, A:G.65, A:H.66, A:V.67, A:V.67, A:V.245, A:V.245, A:R.450, A:G.459, A:Q.461, A:Q.461, A:S.464 Water bridges: A:G.22, A:S.42, A:S.42, A:R.450, A:F.451, A:F.451, A:F.451, A:D.462, A:D.462 pi-Stacking: A:H.66 FDA.4: 30 residues within 4Å: Chain B: I.16, G.17, G.19, P.20, T.21, G.22, D.41, S.42, G.48, L.49, A.50, V.63, G.65, H.66, V.67, G.243, K.244, V.245, T.271, M.272, T.298, E.376, G.421, Y.422, G.449, R.450, G.459, N.460, Q.461, S.464 31 PLIP interactions: 31 interactions with chain B Hydrophobic interactions: B:V.63, B:T.298, B:Y.422 Hydrogen bonds: B:G.19, B:T.21, B:T.21, B:T.21, B:G.22, B:S.42, B:G.47, B:L.49, B:G.65, B:H.66, B:V.67, B:V.67, B:V.245, B:V.245, B:R.450, B:G.459, B:Q.461, B:Q.461, B:S.464 Water bridges: B:S.42, B:S.42, B:A.69, B:R.450, B:F.451, B:F.451, B:F.451, B:D.462 pi-Stacking: B:H.66 FDA.9: 30 residues within 4Å: Chain C: G.17, G.19, P.20, T.21, G.22, D.41, S.42, G.48, L.49, A.50, V.63, G.65, H.66, V.67, 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 26 PLIP interactions: 26 interactions with chain C Hydrophobic interactions: C:T.298, C:Y.422 Hydrogen bonds: C:G.19, C:T.21, C:T.21, C:T.21, C:G.22, C:S.42, C:G.47, C:G.48, C:L.49, C:G.65, C:H.66, C:V.67, C:V.67, C:V.245, C:V.245, C:R.450, C:G.459, C:Q.461, C:Q.461, C:S.464 Water bridges: C:D.41, C:F.451, C:F.451 pi-Stacking: C:H.66 FDA.14: 30 residues within 4Å: Chain D: G.17, G.19, P.20, T.21, D.41, S.42, G.47, G.48, L.49, A.50, V.63, G.65, H.66, V.67, 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 26 PLIP interactions: 26 interactions with chain D Hydrophobic interactions: D:T.298, D:Y.422 Hydrogen bonds: D:G.19, D:T.21, D:T.21, D:T.21, D:S.42, D:G.47, D:L.49, D:G.65, D:H.66, D:V.67, D:V.67, D:V.245, D:V.245, D:R.450, D:G.459, D:Q.461, D:Q.461, D:S.464 Water bridges: D:D.41, D:G.48, D:A.69, D:F.451, D:F.451 pi-Stacking: D:H.66

2 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.2: 16 residues within 4Å: Chain A: V.98, Y.107, P.108, F.109, Q.110, F.161, M.162, Y.165, N.166, W.170, R.185, V.186, Y.320, R.330, Y.422, Y.456 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.107, A:F.161 Hydrogen bonds: A:F.109, A:Q.110, A:Q.110, A:N.166, A:N.166, A:Y.320, A:Y.320, A:Y.456, A:Y.456 Salt bridges: A:R.185, A:R.330, A:R.330 pi-Stacking: A:Y.320 UDP.5: 17 residues within 4Å: Chain B: V.98, Y.107, P.108, F.109, Q.110, F.145, F.161, M.162, Y.165, N.166, W.170, R.185, V.186, Y.320, R.330, Y.422, Y.456 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:Y.107, B:F.161 Hydrogen bonds: B:F.109, B:Q.110, B:Q.110, B:N.166, B:N.166, B:R.185, B:Y.320, B:Y.422, B:Y.456, B:Y.456 Water bridges: B:A.187, B:A.187 Salt bridges: B:R.330, B:R.330 pi-Stacking: B:Y.320

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

SO4.3: 4 residues within 4Å: Chain A: P.310, E.311, R.312, K.405 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.311, A:R.312 Salt bridges: A:R.312, A:K.405 SO4.6: 4 residues within 4Å: Chain B: P.310, E.311, R.312, K.405 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.311, B:R.312 Salt bridges: B:R.312, B:K.405 SO4.7: 2 residues within 4Å: Chain B: N.43, R.416 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.43 Salt bridges: B:R.416 SO4.8: 2 residues within 4Å: Chain B: K.73, R.499 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.499 SO4.10: 4 residues within 4Å: Chain C: P.310, E.311, R.312, K.405 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.312 Water bridges: C:E.311, C:E.311 Salt bridges: C:R.312, C:K.405 SO4.11: 2 residues within 4Å: Chain C: T.155, R.163 2 PLIP interactions: 2 interactions with chain C Water bridges: C:R.163 Salt bridges: C:R.163 SO4.12: 1 residues within 4Å: Chain C: R.499 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.499 SO4.15: 4 residues within 4Å: Chain D: P.310, E.311, R.312, K.405 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.312 Water bridges: D:E.311 Salt bridges: D:R.312, D:K.405 SO4.16: 2 residues within 4Å: Chain D: P.117, K.118 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.118 Salt bridges: D:K.118

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 6 residues within 4Å: Chain C: Q.441, W.446, R.448, N.474, E.481, N.485 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:N.474, C:N.474, C:E.481, C:N.485, C:N.485 Water bridges: A:E.497, A:E.497 GOL.17: 5 residues within 4Å: Chain D: Q.441, W.446, N.474, E.481, N.485 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:N.474, D:N.474, D:N.485, D:N.485 Water bridges: D:E.481

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Da Fonseca, I. et al., Contributions of Unique Active Site Residues of Eukaryotic UDP-Galactopyranose Mutases to Substrate Recognition and Active Site Dynamics. Biochemistry (2014)

Release Date

2014-12-03

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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