SMTL ID : 5eqd.1 (2 other biounits)

Structure of oxidized UDP-galactopyranose mutase from Mycobacterium smegmatis in complex with UDP in opened and closed form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 35 residues within 4Å: Chain A: V.10, G.11, S.12, G.13, F.14, F.15, I.34, E.35, R.36, R.37, G.42, N.43, Y.59, G.60, A.61, H.62, L.63, T.220, D.221, W.222, F.223, T.241, G.242, P.243, R.246, L.260, Y.324, Y.325, G.356, R.357, Y.363, L.364, D.365, M.366, A.369 36 PLIP interactions: 36 interactions with chain A Hydrophobic interactions: A:N.43, A:L.260, A:Y.324, A:Y.363 Hydrogen bonds: A:S.12, A:G.13, A:F.15, A:R.36, A:R.37, A:G.42, A:N.43, A:H.62, A:L.63, A:L.63, A:D.221, A:D.221, A:W.222, A:T.241, A:R.246, A:R.357, A:Y.363, A:M.366 Water bridges: A:F.14, A:F.14, A:G.16, A:G.16, A:R.36, A:N.43, A:N.43, A:R.357, A:R.357, A:L.358, A:H.367 Salt bridges: A:R.357 pi-Stacking: A:H.62 pi-Cation interactions: A:H.62 FAD.9: 34 residues within 4Å: Chain B: V.10, G.11, S.12, G.13, F.14, F.15, I.34, E.35, R.36, R.37, G.42, N.43, Y.59, A.61, H.62, L.63, T.220, D.221, W.222, F.223, T.241, G.242, P.243, R.246, L.260, Y.324, Y.325, G.356, R.357, L.358, L.364, D.365, M.366, A.369 32 PLIP interactions: 32 interactions with chain B Hydrophobic interactions: B:L.260, B:Y.324 Hydrogen bonds: B:G.13, B:F.14, B:F.15, B:R.36, B:R.37, B:G.42, B:N.43, B:H.62, B:L.63, B:L.63, B:D.221, B:W.222, B:R.246, B:R.357, B:D.365, B:M.366 Water bridges: B:R.36, B:R.36, B:N.43, B:N.43, B:N.43, B:N.43, B:R.177, B:T.241, B:R.289, B:Y.325, B:L.358, B:L.358 pi-Stacking: B:H.62 pi-Cation interactions: B:H.62

7 x NO3: NITRATE ION(Non-functional Binders)

NO3.2: 7 residues within 4Å: Chain A: S.46, E.55, H.57, P.197, G.200, Y.201, H.297 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.46, A:S.46, A:Y.201, A:H.297 NO3.3: 1 residues within 4Å: Chain A: R.120 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.120, A:R.120 NO3.5: 3 residues within 4Å: Chain A: E.265, I.309, R.311 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.311 Water bridges: A:Y.287, A:R.311 NO3.7: 4 residues within 4Å: Chain A: E.21, T.25, Q.77, F.78 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.22, A:Q.26 NO3.10: 7 residues within 4Å: Chain B: S.46, E.55, H.57, P.197, G.200, Y.201, H.297 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.46, B:S.46, B:Y.201, B:H.297 NO3.11: 1 residues within 4Å: Chain B: R.120 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.120, B:R.120 NO3.12: 7 residues within 4Å: Chain B: M.91, H.92, N.93, G.94, D.282, D.284, V.285 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.94, B:D.282, B:D.282 Water bridges: B:N.93, B:N.93

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

SO4.4: 1 residues within 4Å: Chain A: R.70 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.70, A:R.70 Salt bridges: A:R.70 SO4.6: 3 residues within 4Å: Chain A: E.152, K.156, H.157 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.156, A:H.157 SO4.13: 2 residues within 4Å: Chain B: A.251, R.342 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.342 SO4.14: 4 residues within 4Å: Chain B: P.171, A.172, S.173, R.333 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.172, B:S.173, B:S.173 Salt bridges: B:R.333 SO4.15: 3 residues within 4Å: Chain B: K.69, D.73, R.76 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.76 Salt bridges: B:K.69, B:R.76 SO4.16: 1 residues within 4Å: Chain B: R.112 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.112, B:R.112 Salt bridges: B:R.112

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

UDP.8: 17 residues within 4Å: Chain B: F.99, F.138, F.154, I.155, Y.158, T.159, Q.162, W.163, N.174, R.177, L.178, Y.188, N.279, N.281, R.289, Y.325, Y.363 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:F.99 Hydrogen bonds: B:F.154, B:T.159, B:T.159, B:T.159, B:N.279, B:N.281, B:Y.325, B:Y.363 Water bridges: B:Q.162, B:N.174, B:R.177, B:R.177, B:R.177, B:R.177, B:R.177, B:R.289, B:R.289, B:R.289, B:R.289, B:D.365 Salt bridges: B:R.177, B:R.177, B:R.289 pi-Stacking: B:Y.158

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wangkanont, K. et al., Structural dynamics of UDP-galactopyranose mutase from Mycobacterium smegmatis. to be published

Release Date

2016-11-23

Peptides

UDP-galactopyranose mutase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

UDP-galactopyranose mutase

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