SMTL ID : 1kvq.1

UDP-GALACTOSE 4-EPIMERASE COMPLEXED WITH UDP-PHENOL

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 1 residues within 4Å: Chain A: Q.91 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.91 NA.2: 1 residues within 4Å: Chain A: Q.334 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.334 Water bridges: A:Q.194, A:Q.194 NA.6: 1 residues within 4Å: Chain B: Q.91 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:Q.91, A:K.165, A:A.166 NA.7: 1 residues within 4Å: Chain B: Q.334 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.334 Water bridges: B:Q.194, B:Q.194

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

NAD.3: 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, A.124, Y.149, K.153, Y.177, F.178, P.180 Ligands: UPG.4 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:A.124, A:Y.177, A:P.180 Hydrogen bonds: A:Y.11, A:I.12, A:G.13, A:N.32, A:N.32, A:L.33, A:C.34, A:N.35, A:N.35, A:S.36, A:S.36, A:I.59, A:F.80, A:G.82, A:N.99, A:S.122, A:Y.149, A:K.153 Water bridges: A:G.10, A:L.83, A:K.84, A:N.99, A:K.153, A:P.180, A:N.199, A:N.199 Salt bridges: A:K.84, A:K.84 NAD.8: 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, A.124, Y.149, K.153, Y.177, F.178, P.180 Ligands: UPG.9 30 PLIP interactions: 30 interactions with chain B Hydrophobic interactions: B:A.124, B:Y.177, B:P.180 Hydrogen bonds: B:Y.11, B:I.12, B:G.13, B:N.32, B:N.32, B:L.33, B:C.34, B:N.35, B:N.35, B:S.36, B:S.36, B:I.59, B:F.80, B:G.82, B:N.99, B:S.122, B:K.153 Water bridges: B:G.10, B:L.83, B:K.84, B:N.99, B:K.153, B:P.180, B:N.199, B:N.199 Salt bridges: B:K.84, B:K.84

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

UPG.4: 22 residues within 4Å: Chain A: A.124, A.125, T.126, Y.149, Y.177, 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.3 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:F.218 Hydrogen bonds: A:T.126, A:N.179, A:N.199, A:N.199, A:L.200, A:A.216, A:F.218, A:Y.233, A:D.295, A:Y.299 Water bridges: A:T.126, A:M.201, A:G.229, A:R.231, A:R.231, A:R.231, A:D.295 Salt bridges: A:R.231, A:R.292, A:R.292 UPG.9: 22 residues within 4Å: Chain B: A.124, A.125, T.126, Y.149, Y.177, 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.8 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:F.218 Hydrogen bonds: B:T.126, B:Y.149, B:N.179, B:N.199, B:N.199, B:L.200, B:A.216, B:F.218, B:D.295, B:Y.299 Water bridges: B:M.201, B:G.229, 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 EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 4 residues within 4Å: Chain A: S.214, N.285, Y.286, H.287 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.214, A:S.214, A:N.285, A:H.287 EDO.10: 4 residues within 4Å: Chain B: S.214, N.285, Y.286, H.287 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.214, B:S.214, B:N.285

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thoden, J.B. et al., Molecular structures of the S124A, S124T, and S124V site-directed mutants of UDP-galactose 4-epimerase from Escherichia coli. Biochemistry (1997)

Release Date

1998-06-17

Peptides

UDP-GALACTOSE 4-EPIMERASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

UDP-GALACTOSE 4-EPIMERASE