SMTL ID : 2y0c.1 (1 other biounit)

BceC mutation Y10S

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x UGA: URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID(Non-covalent)

UGA.1: 21 residues within 4Å: Chain A: E.162, F.163, L.164, K.165, E.166, K.222, N.226, I.233, F.267, L.268, Y.269, G.273, Y.274, G.275, C.278, F.279, F.338, K.339, R.439 Chain B: R.262 Ligands: TRS.9 21 PLIP interactions: 19 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.233, A:F.267 Hydrogen bonds: A:F.163, A:E.166, A:K.222, A:N.226, A:N.226, A:Y.269, A:Y.269, A:G.275, A:G.275, A:F.338, A:R.439, B:R.262, B:R.262 Water bridges: A:E.166, A:E.166, A:K.339 Salt bridges: A:K.222, A:K.339, A:K.339 UGA.10: 21 residues within 4Å: Chain A: R.262 Chain B: E.162, F.163, L.164, K.165, E.166, K.222, N.226, I.233, F.267, L.268, Y.269, G.273, Y.274, G.275, C.278, F.279, D.282, F.338, K.339, R.439 20 PLIP interactions: 18 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.233, B:F.267 Hydrogen bonds: B:F.163, B:E.166, B:K.222, B:N.226, B:N.226, B:Y.269, B:Y.269, B:G.275, B:G.275, B:F.338, B:R.439, A:R.262, A:R.262 Water bridges: B:E.162, B:E.162 Salt bridges: B:K.222, B:K.339, B:K.339

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

SO4.2: 2 residues within 4Å: Chain A: R.346, R.351 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.347 Salt bridges: A:R.346, A:R.351 SO4.3: 2 residues within 4Å: Chain A: R.254, R.255 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.254 Salt bridges: A:R.254, A:R.255 SO4.4: 3 residues within 4Å: Chain A: R.193, K.197, Y.212 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Y.212 Salt bridges: A:R.193, A:K.197 SO4.5: 4 residues within 4Å: Chain A: G.133, R.216, H.293 Chain B: F.246 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.216, A:H.293 SO4.11: 2 residues within 4Å: Chain B: H.266, Y.269 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.266 SO4.12: 4 residues within 4Å: Chain B: R.312, E.356, S.359, R.360 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.359 Salt bridges: B:R.312, B:R.360 SO4.13: 3 residues within 4Å: Chain B: R.193, E.194, K.197 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.193, B:K.197 SO4.14: 1 residues within 4Å: Chain B: R.428 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.428 SO4.17: 1 residues within 4Å: Chain B: R.363 4 PLIP interactions: 4 interactions with chain B Water bridges: B:G.328, B:G.328, B:G.328 Salt bridges: B:R.363

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 6 residues within 4Å: Chain A: D.172, F.173, P.176, I.179, Y.200, F.203 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.173, A:I.179, A:Y.200, A:F.203 Water bridges: A:Y.200 ACT.15: 6 residues within 4Å: Chain B: D.172, F.173, P.176, I.179, Y.200, F.203 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.173, B:I.179, B:Y.200, B:F.203 Hydrogen bonds: B:F.173

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: G.120, F.121, M.154, R.191 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.121, A:R.191, A:R.191 GOL.8: 4 residues within 4Å: Chain A: Y.265, H.266, F.267, Y.269 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.266, A:F.267, A:Y.269 Water bridges: A:R.254, A:L.268 GOL.16: 3 residues within 4Å: Chain B: R.346, E.347, R.351 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.347, B:E.347, B:R.351, B:R.351 Water bridges: B:V.378, B:D.382

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.9: 7 residues within 4Å: Chain A: F.163, K.165, D.177, R.178 Chain B: D.260, R.262 Ligands: UGA.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.163, A:D.177, A:R.178

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rocha, J. et al., Structure of Burkholderia Cepacia Udp-Glucose Dehydrogenase (Ugd) Bcec and Role of Tyr10 in Final Hydrolysis of Ugd Thioester Intermediate. J.Bacteriol. (2011)

Release Date

2011-07-27

Peptides

UDP-GLUCOSE DEHYDROGENASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

UDP-GLUCOSE DEHYDROGENASE

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