SMTL ID : 2y0c.2 (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: 20 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 19 PLIP interactions: 17 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: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:S.277 Salt bridges: A:K.222, A:K.339, A:K.339 UGA.7: 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, F.338, K.339, R.439 Ligands: GOL.13 19 PLIP interactions: 17 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:Y.269, B:Y.269, B:G.275, B:G.275, B:D.282, B:F.338, B:R.439, A:R.262, A:R.262 Water bridges: B:F.163 Salt bridges: B:K.222, B:K.339, B:K.339

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

SO4.2: 2 residues within 4Å: Chain A: R.254, R.255 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.254, A:R.254 Salt bridges: A:R.254 SO4.3: 3 residues within 4Å: Chain A: G.120, F.121, R.191 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.121 Salt bridges: A:R.191 SO4.6: 2 residues within 4Å: Chain B: G.451, Q.464 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.463, B:Q.464 SO4.8: 2 residues within 4Å: Chain B: H.266, Y.269 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.269 Water bridges: B:F.267 Salt bridges: B:H.266 SO4.9: 2 residues within 4Å: Chain B: R.346, R.351 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.351 Salt bridges: B:R.351

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

ACT.4: 6 residues within 4Å: Chain A: D.172, F.173, P.176, I.179, Y.200, F.203 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.173, A:P.176, A:I.179, A:Y.200, A:F.203 Water bridges: A:Y.200 ACT.10: 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 ACT.11: 7 residues within 4Å: Chain A: F.246 Chain B: P.131, V.132, Y.223, A.285, L.286, T.289 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.223, B:L.286 Hydrogen bonds: B:V.132, B:T.289

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: Y.265, H.266, F.267, Y.269 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.265, A:F.267 Water bridges: A:L.268 GOL.12: 4 residues within 4Å: Chain B: G.120, F.121, M.154, R.191 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.121, B:M.154, B:R.191, B:R.191 GOL.13: 9 residues within 4Å: Chain B: S.18, V.19, E.56, E.162, L.164, E.166, A.169, C.278 Ligands: UGA.7 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.18, B:S.18, B:E.56, B:L.164, B:E.166 Water bridges: B:R.346

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
C

B
D

UDP-GLUCOSE DEHYDROGENASE

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