SMTL ID : 1udc.1

STRUCTURE OF UDP-GALACTOSE-4-EPIMERASE COMPLEXED WITH UDP-MANNOSE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

6 x NA: SODIUM ION(Non-functional Binders)

NA.1: 1 residues within 4Å: Chain A: Q.91 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.166, A:Q.91 NA.2: 1 residues within 4Å: Chain A: Q.194 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.194 NA.3: 2 residues within 4Å: Chain A: Q.334, Y.336 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.336 Water bridges: A:K.37 NA.10: 1 residues within 4Å: Chain B: Q.91 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:A.166, B:Q.91 NA.11: 1 residues within 4Å: Chain B: Q.194 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.194, B:Q.194 NA.12: 2 residues within 4Å: Chain B: Q.334, Y.336 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.336 Water bridges: B:K.37

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.4: 29 residues within 4Å: Chain A: G.7, S.9, G.10, Y.11, I.12, D.31, N.32, L.33, C.34, N.35, S.36, G.57, D.58, I.59, R.60, F.80, A.81, G.82, K.84, N.99, S.122, S.123, S.124, Y.149, K.153, Y.177, P.180 Ligands: UFM.5, EDO.7 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:Y.177 Hydrogen bonds: A:G.7, A:Y.11, A:I.12, A:N.32, A:N.32, A:L.33, A:C.34, A:N.35, A:N.35, A:S.36, A:D.58, A:I.59, A:R.60, A:F.80, A:G.82, A:K.84, A:S.122, A:Y.149, A:K.153 Water bridges: A:G.10, A:G.13, A:L.83, A:K.84, A:N.99, A:K.153, A:N.199, A:N.199 Salt bridges: A:K.84, A:K.84 NAD.13: 29 residues within 4Å: Chain B: G.7, S.9, G.10, Y.11, I.12, D.31, N.32, L.33, C.34, N.35, S.36, G.57, D.58, I.59, R.60, F.80, A.81, G.82, K.84, N.99, S.122, S.123, S.124, Y.149, K.153, Y.177, P.180 Ligands: UFM.14, EDO.16 29 PLIP interactions: 29 interactions with chain B Hydrophobic interactions: B:Y.177 Hydrogen bonds: B:G.7, B:Y.11, B:I.12, B:N.32, B:N.32, B:L.33, B:C.34, B:N.35, B:N.35, B:S.36, B:D.58, B:I.59, B:R.60, B:F.80, B:G.82, B:K.84, B:S.122, B:K.153 Water bridges: B:G.10, B:G.13, B:L.83, B:K.84, B:N.99, B:K.153, B:N.199, B:N.199 Salt bridges: B:K.84, B:K.84

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

UFM.5: 22 residues within 4Å: Chain A: V.86, S.124, T.126, Y.149, F.178, N.179, N.198, N.199, L.200, L.215, A.216, I.217, F.218, G.229, R.231, Y.233, V.269, R.292, D.295, Y.299 Ligands: NAD.4, EDO.9 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:F.218 Hydrogen bonds: A:T.126, A:N.179, A:N.179, A:N.199, A:N.199, A:L.200, A:A.216, A:F.218, A:Y.233, A:Y.299 Water bridges: A:T.126, A:M.201, A:A.216, A:R.231, A:R.231, A:R.231, A:D.295, A:D.295 Salt bridges: A:R.231, A:R.292, A:R.292 UFM.14: 22 residues within 4Å: Chain B: V.86, S.124, T.126, Y.149, F.178, N.179, N.198, N.199, L.200, L.215, A.216, I.217, F.218, G.229, R.231, Y.233, V.269, R.292, D.295, Y.299 Ligands: NAD.13, EDO.18 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:F.218 Hydrogen bonds: B:T.126, B:T.126, B:N.179, B:N.179, B:N.199, B:N.199, B:L.200, B:A.216, B:F.218, B:Y.299 Water bridges: B:M.201, B:A.216, B:R.231, B:R.231, B:R.231, B:D.295 Salt bridges: B:R.231, B:R.292, B:R.292

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.6: 5 residues within 4Å: Chain A: L.250, K.253, Y.259, E.309, L.310 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.253, A:Y.259 PGE.15: 5 residues within 4Å: Chain B: L.250, K.253, Y.259, E.309, L.310 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.253

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 7 residues within 4Å: Chain A: Y.11, N.35, G.190, E.191, D.192, P.193 Ligands: NAD.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.192 Water bridges: A:G.10, A:N.35, A:N.35 EDO.8: 6 residues within 4Å: Chain A: L.94, E.95, D.98 Chain B: L.105, R.106, S.109 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Water bridges: A:L.94, A:E.95, A:D.98 Hydrogen bonds: B:R.106, B:S.109 EDO.9: 7 residues within 4Å: Chain A: K.84, A.85, V.86, N.198, N.199, R.292 Ligands: UFM.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.84, A:V.86, A:N.199, A:R.292, A:R.292 Water bridges: A:R.292 EDO.16: 7 residues within 4Å: Chain B: Y.11, N.35, G.190, E.191, D.192, P.193 Ligands: NAD.13 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.35, B:D.192 Water bridges: B:G.10, B:N.35 EDO.17: 6 residues within 4Å: Chain A: L.105, R.106, S.109 Chain B: L.94, E.95, D.98 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Water bridges: B:L.94, B:E.95, B:E.95 Hydrogen bonds: A:R.106, A:S.109 EDO.18: 7 residues within 4Å: Chain B: K.84, A.85, V.86, N.198, N.199, R.292 Ligands: UFM.14 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.84, B:V.86, B:R.292, B:R.292 Water bridges: B:R.292

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thoden, J.B. et al., Structural analysis of UDP-sugar binding to UDP-galactose 4-epimerase from Escherichia coli. Biochemistry (1997)

Release Date

1998-01-14

Peptides

UDP-GALACTOSE-4-EPIMERASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

UDP-GALACTOSE-4-EPIMERASE

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