SMTL ID : 3ukf.1 (1 other biounit)

CRYSTAL STRUCTURE OF UDP-galactopyranose mutase from Aspergillus fumigatus in complex with UDPgalp (reduced)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 x GDU: GALACTOSE-URIDINE-5'-DIPHOSPHATE(Non-covalent)

GDU.1: 21 residues within 4Å: Chain A: G.60, G.61, F.65, V.94, Y.103, P.104, F.105, Q.106, F.157, M.158, N.162, W.166, R.181, V.182, N.206, Y.316, R.326, Y.418, Y.452, N.456 Ligands: FDA.2 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:Y.103, A:F.157 Hydrogen bonds: A:G.61, A:F.105, A:Q.106, A:Q.106, A:N.162, A:N.162, A:R.181, A:N.206, A:N.206, A:Y.316, A:Y.316, A:Y.418, A:Y.452 Water bridges: A:A.183, A:A.183, A:Y.418, A:R.446, A:R.446, A:N.456 Salt bridges: A:R.326, A:R.326 pi-Stacking: A:Y.316 GDU.5: 21 residues within 4Å: Chain B: G.60, G.61, F.65, Y.103, P.104, F.105, Q.106, F.157, M.158, Y.161, N.162, W.166, R.181, V.182, N.206, Y.316, R.326, Y.418, Y.452, N.456 Ligands: FDA.6 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:Y.103, B:F.157 Hydrogen bonds: B:G.61, B:F.105, B:Q.106, B:Q.106, B:N.162, B:N.162, B:R.181, B:R.181, B:N.206, B:N.206, B:Y.316, B:Y.452, B:Y.452 Water bridges: B:A.183, B:A.183, B:Y.418, B:R.446 Salt bridges: B:R.181, B:R.326, B:R.326, B:R.326 pi-Stacking: B:Y.316 GDU.8: 22 residues within 4Å: Chain C: G.60, G.61, F.65, V.94, Y.103, P.104, F.105, Q.106, F.157, M.158, Y.161, N.162, W.166, R.181, V.182, N.206, Y.316, R.326, Y.418, Y.452, N.456 Ligands: FDA.9 24 PLIP interactions: 24 interactions with chain C Hydrophobic interactions: C:Y.103, C:F.157 Hydrogen bonds: C:G.61, C:F.105, C:Q.106, C:Q.106, C:N.162, C:N.162, C:R.181, C:N.206, C:N.206, C:Y.316, C:Y.316, C:Y.418, C:Y.452 Water bridges: C:R.181, C:Y.418, C:R.446, C:R.446 Salt bridges: C:R.181, C:R.326, C:R.326, C:R.326 pi-Stacking: C:Y.316 GDU.10: 21 residues within 4Å: Chain D: G.60, G.61, F.65, Y.103, P.104, F.105, Q.106, F.157, M.158, Y.161, N.162, W.166, R.181, V.182, N.206, Y.316, R.326, Y.418, Y.452, N.456 Ligands: FDA.11 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:Y.103, D:F.157 Hydrogen bonds: D:G.61, D:F.105, D:Q.106, D:Q.106, D:N.162, D:N.162, D:R.181, D:N.206, D:N.206, D:Y.316, D:Y.452, D:Y.452 Water bridges: D:Y.103, D:A.183, D:Y.418, D:R.446, D:R.446, D:N.456 Salt bridges: D:R.326, D:R.326

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

FDA.2: 27 residues within 4Å: Chain A: G.13, G.15, P.16, T.17, D.37, S.38, G.44, L.45, A.46, V.59, G.61, H.62, V.63, G.239, K.240, V.241, M.268, E.372, G.417, Y.418, G.445, R.446, G.455, N.456, Q.457, S.460 Ligands: GDU.1 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:Y.418 Hydrogen bonds: A:A.14, A:G.15, A:T.17, A:T.17, A:T.17, A:S.38, A:L.45, A:A.46, A:H.62, A:V.63, A:V.63, A:V.241, A:V.241, A:R.446, A:G.455, A:Q.457, A:S.460 Water bridges: A:G.18, A:R.446, A:F.447, A:F.447 FDA.6: 28 residues within 4Å: Chain B: I.12, G.13, G.15, P.16, T.17, D.37, S.38, G.44, L.45, A.46, V.59, G.61, H.62, V.63, G.239, K.240, V.241, M.268, E.372, G.417, Y.418, G.445, R.446, G.455, N.456, Q.457, S.460 Ligands: GDU.5 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:Y.418 Hydrogen bonds: B:A.14, B:G.15, B:T.17, B:T.17, B:T.17, B:S.38, B:L.45, B:H.62, B:V.63, B:V.63, B:V.241, B:V.241, B:R.446, B:G.455, B:Q.457, B:S.460 Water bridges: B:G.18, B:T.267, B:F.447, B:F.447 FDA.9: 30 residues within 4Å: Chain C: I.12, G.13, A.14, G.15, P.16, T.17, D.37, S.38, G.44, L.45, A.46, V.59, G.61, H.62, V.63, G.239, K.240, V.241, T.267, M.268, E.372, G.417, Y.418, G.445, R.446, G.455, N.456, Q.457, S.460 Ligands: GDU.8 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:Y.418 Hydrogen bonds: C:A.14, C:G.15, C:T.17, C:T.17, C:S.38, C:L.45, C:H.62, C:V.63, C:V.63, C:V.241, C:V.241, C:R.446, C:G.455, C:Q.457, C:S.460 Water bridges: C:G.44, C:T.267, C:F.447, C:F.447 FDA.11: 27 residues within 4Å: Chain D: G.13, G.15, P.16, T.17, D.37, S.38, G.43, G.44, L.45, A.46, V.59, H.62, V.63, G.239, K.240, V.241, M.268, E.372, G.417, Y.418, G.445, R.446, G.455, N.456, Q.457, S.460 Ligands: GDU.10 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:Y.418 Hydrogen bonds: D:A.14, D:G.15, D:T.17, D:T.17, D:T.17, D:S.38, D:L.45, D:V.63, D:V.63, D:V.241, D:V.241, D:R.446, D:G.455, D:Q.457, D:S.460 Water bridges: D:G.43

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 3 residues within 4Å: Chain A: D.84, A.213, R.214 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: A.475, V.476 Chain B: R.494 Ligands: CL.7 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: R.494 Chain B: A.475, V.476 Ligands: CL.4 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain C: R.494 Chain D: A.475, V.476 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

van Straaten, K.E. et al., Structural Insight into the Unique Substrate Binding Mechanism and Flavin Redox State of UDP-galactopyranose Mutase from Aspergillus fumigatus. J.Biol.Chem. (2012)

Release Date

2012-02-22

Peptides

UDP-galactopyranose mutase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
C

D
F

UDP-galactopyranose mutase

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