SMTL ID : 5hhf.1

Crystal structure of Aspergillus fumigatus UDP-Galactopyranose mutase mutant H63A with covalent FAD-Galactopyranose and bound UDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: P.310, E.311, R.312, K.405 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.312 Water bridges: A:E.311, A:E.311 Salt bridges: A:R.312, A:K.405 SO4.5: 4 residues within 4Å: Chain B: P.310, E.311, R.312, K.405 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.312 Water bridges: B:E.311, B:E.311 Salt bridges: B:R.312, B:K.405 SO4.6: 2 residues within 4Å: Chain B: K.73, R.499 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.73, B:R.499 SO4.10: 3 residues within 4Å: Chain C: P.310, E.311, R.312 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 1 PLIP interactions: 1 interactions with chain C 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 SO4.13: 2 residues within 4Å: Chain C: P.117, K.118 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.118 Salt bridges: C:K.118 SO4.16: 4 residues within 4Å: Chain D: P.310, E.311, R.312, K.405 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.312 Water bridges: D:E.311, D:E.311 Salt bridges: D:R.312, D:K.405 SO4.17: 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 SO4.18: 2 residues within 4Å: Chain D: T.155, R.163 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.155 Water bridges: D:D.159 Salt bridges: D:R.163

4 x MRY: MESO-ERYTHRITOL(Non-covalent)

MRY.2: 5 residues within 4Å: Chain A: Q.441, W.446, N.474, E.481, N.485 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.441, A:W.446, A:N.474, A:N.474, A:N.485 MRY.7: 5 residues within 4Å: Chain B: Q.441, W.446, N.474, E.481, N.485 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.441, B:W.446, B:N.474, B:N.474, B:E.481, B:N.485 Water bridges: B:Q.441 MRY.14: 5 residues within 4Å: Chain C: Q.441, W.446, N.474, E.481, N.485 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.441, C:N.474, C:N.474, C:E.481, C:N.485 MRY.19: 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:Q.441, D:W.446, D:N.474, D:N.474, D:N.485

2 x 62F: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{S})-5-[5-[(2~{R},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-7,8-dimethyl-2,4-bis(oxidanyl)benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate(Non-covalent)

62F.3: 34 residues within 4Å: Chain A: G.17, G.19, P.20, T.21, D.41, S.42, G.48, L.49, A.50, G.64, G.65, A.66, V.67, F.69, R.185, N.210, G.243, K.244, V.245, T.271, M.272, W.318, Y.329, R.330, E.376, G.421, Y.422, G.449, R.450, G.459, N.460, Q.461, S.464 Ligands: UDP.4 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:Y.422 Hydrogen bonds: A:G.19, A:T.21, A:T.21, A:T.21, A:S.42, A:L.49, A:L.49, A:V.67, A:V.67, A:R.185, A:N.210, A:V.245, A:V.245, A:R.450, A:N.460, A:N.460, A:Q.461, A:Q.461, A:S.464 Water bridges: A:G.22, A:T.271, A:R.450, A:F.451, A:F.451, A:N.460 62F.8: 35 residues within 4Å: Chain B: G.17, G.19, P.20, T.21, D.41, S.42, G.48, L.49, A.50, V.63, G.64, G.65, A.66, V.67, F.69, R.185, N.210, G.243, K.244, V.245, T.271, M.272, W.318, Y.329, R.330, E.376, G.421, Y.422, G.449, R.450, G.459, N.460, Q.461, S.464 Ligands: UDP.9 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:Y.422 Hydrogen bonds: B:G.19, B:T.21, B:T.21, B:T.21, B:S.42, B:L.49, B:L.49, B:V.67, B:V.67, B:R.185, B:N.210, B:V.245, B:V.245, B:R.450, B:N.460, B:N.460, B:Q.461, B:Q.461, B:D.462, B:S.464 Water bridges: B:G.22, B:G.48, B:R.450, B:F.451, B:F.451, B:N.460

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

UDP.4: 18 residues within 4Å: Chain A: V.98, Y.107, F.109, Q.110, F.145, F.161, M.162, Y.165, N.166, V.169, W.170, R.185, V.186, Y.320, R.330, Y.422, Y.456 Ligands: 62F.3 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:Y.107, A:F.161 Hydrogen bonds: A:F.109, A:Q.110, A:Q.110, A:Y.165, A:N.166, A:N.166, A:R.185, A:Y.320, A:Y.320, A:Y.456, A:Y.456 Water bridges: A:A.187, A:A.187, A:N.210, A:N.210 Salt bridges: A:R.330, A:R.330 pi-Stacking: A:Y.320 UDP.9: 19 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, V.169, W.170, R.185, V.186, Y.320, R.330, Y.422, Y.456 Ligands: 62F.8 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 Water bridges: B:R.185, B:Y.320, B:Y.320 Salt bridges: B:R.330, B:R.330 pi-Stacking: B:Y.320

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

FDA.15: 26 residues within 4Å: Chain C: G.17, G.19, P.20, T.21, D.41, S.42, G.48, L.49, A.50, A.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 25 PLIP interactions: 25 interactions with chain C Hydrophobic interactions: C:L.49, C:T.298, C:Y.422 Hydrogen bonds: C:G.19, C:T.21, C:T.21, C:T.21, C:S.42, C:L.49, C:L.49, C:A.66, C:V.67, C:V.67, C:V.245, C:V.245, C:R.450, C:N.460, C:Q.461, C:Q.461, C:S.464 Water bridges: C:G.22, C:G.48, C:T.271, C:F.451, C:F.451 FDA.20: 27 residues within 4Å: Chain D: G.17, G.19, P.20, T.21, D.41, S.42, G.48, L.49, A.50, V.63, A.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 25 PLIP interactions: 25 interactions with chain D Hydrophobic interactions: D:L.49, D:V.63, D:T.298, D:Y.422 Hydrogen bonds: D:G.19, D:T.21, D:T.21, D:T.21, D:S.42, D:L.49, D:L.49, D:V.67, D:V.67, D:V.245, D:V.245, D:T.271, D:R.450, D:N.460, D:Q.461, D:Q.461, D:S.464 Water bridges: D:G.22, D:F.451, D:F.451 pi-Cation interactions: D:R.450

Links

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Citation

Mehra-Chaudhary, R. et al., In Crystallo Capture of a Covalent Intermediate in the UDP-Galactopyranose Mutase Reaction. Biochemistry (2016)

Release Date

2016-02-17

Peptides

UDP-galactopyranose mutase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

UDP-galactopyranose mutase