SMTL ID : 5er9.1 (2 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

homo-dimer

Ligands

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

UDP.1: 11 residues within 4Å: Chain A: F.99, F.154, I.155, Y.158, T.159, Q.162, Y.188, N.279, N.281, R.289, Y.325 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.99 Hydrogen bonds: A:F.154, A:T.159, A:Q.162, A:Q.162, A:Y.188, A:Y.188, A:N.279, A:N.281 Water bridges: A:Y.158, A:R.289, A:R.289, A:R.289, A:E.312 Salt bridges: A:R.289 pi-Stacking: A:Y.158 UDP.9: 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 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:F.99 Hydrogen bonds: B:F.154, B:T.159, B:T.159, B:T.159, B:W.163, 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

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

FAD.2: 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.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:R.36, A:N.43, A:N.43, A:R.289, A:L.358 Salt bridges: A:R.357 pi-Stacking: A:H.62 pi-Cation interactions: A:H.62 FAD.10: 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 34 PLIP interactions: 34 interactions with chain B Hydrophobic interactions: B:N.43, B:L.260, B:Y.324 Hydrogen bonds: B:G.13, B:F.14, B:F.15, B:R.36, B:R.37, B:R.37, B:N.43, B:N.43, B:H.62, B:L.63, B:L.63, B:D.221, B:W.222, B:R.246, B:R.246, B:R.357, B:D.365, B:M.366 Water bridges: B:G.16, B:R.37, B:G.42, B:N.43, B:R.177, B:T.241, B:R.289, B:R.357, B:R.357, B:L.358, B:L.358 pi-Stacking: B:H.62 pi-Cation interactions: B:H.62

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

NO3.3: 8 residues within 4Å: Chain A: S.46, E.55, H.57, L.196, 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 NO3.4: 3 residues within 4Å: Chain A: R.294, H.295, P.298 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.294 Water bridges: A:G.270, A:R.294 NO3.5: 4 residues within 4Å: Chain A: T.269, G.270, D.271, T.304 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.269, A:T.269, A:G.270, A:D.271 Water bridges: A:T.304 NO3.6: 1 residues within 4Å: Chain A: R.120 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.120, A:R.120 NO3.11: 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:Y.201, B:H.297 Water bridges: B:E.55 NO3.12: 1 residues within 4Å: Chain B: R.120 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.120, B:R.120

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

SO4.7: 1 residues within 4Å: Chain A: R.70 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.70 SO4.8: 5 residues within 4Å: Chain A: H.92, N.93, F.109, E.152, A.153 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.93 Salt bridges: A:H.92 SO4.13: 3 residues within 4Å: Chain B: K.69, D.73, R.76 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.69, B:R.76 SO4.14: 2 residues within 4Å: Chain B: A.251, R.342 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.342 SO4.15: 3 residues within 4Å: Chain B: P.171, A.172, S.173 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.173, B:S.173 Water bridges: B:A.172, B:A.172 SO4.16: 2 residues within 4Å: Chain B: Q.85, R.187 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Water bridges: B:Q.85, B:Q.85, B:R.187, B:R.187, A:G.83 Salt bridges: B:R.187 Hydrogen bonds: A:G.83 SO4.17: 1 residues within 4Å: Chain B: R.112 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.112

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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