SMTL ID : 2z86.2 (1 other biounit)

Crystal structure of chondroitin polymerase from Escherichia coli strain K4 (K4CP) complexed with UDP-GlcUA and UDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

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

UDP.1: 13 residues within 4Å: Chain A: P.100, T.101, Y.102, R.104, D.131, Y.160, L.162, V.165, D.182, C.183, D.184, H.329 Ligands: MN.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.102, A:Y.160 Hydrogen bonds: A:P.100, A:Y.102, A:D.131, A:C.183 Water bridges: A:R.104, A:R.104, A:Y.160 Salt bridges: A:R.104

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

UGA.2: 21 residues within 4Å: Chain A: P.382, A.383, Y.384, D.412, N.439, G.441, I.442, A.445, Q.460, D.462, S.463, D.464, H.524, R.526, N.545, A.546, V.547, D.548, R.571, H.574 Ligands: MN.4 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:I.442 Hydrogen bonds: A:Y.384, A:D.412, A:D.412, A:G.441, A:D.462, A:D.462, A:S.463, A:S.463, A:S.463, A:R.526, A:A.546, A:V.547, A:D.548, A:R.571 Water bridges: A:D.462 Salt bridges: A:H.574, A:H.574 UGA.5: 20 residues within 4Å: Chain B: P.100, T.101, Y.102, R.104, D.131, G.159, Y.160, L.162, V.165, R.166, D.182, C.183, D.184, R.211, G.278, G.279, E.304, D.305, H.329 Ligands: MN.7 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:Y.102, B:Y.160 Hydrogen bonds: B:D.131, B:Y.160, B:Q.161, B:R.166, B:R.166, B:D.182, B:D.182, B:C.183, B:G.278, B:D.305 Water bridges: B:R.211, B:G.279 Salt bridges: B:R.104, B:R.211 UGA.6: 21 residues within 4Å: Chain B: P.382, A.383, Y.384, D.412, N.439, G.441, I.442, A.445, Q.460, D.462, S.463, D.464, H.524, R.526, N.545, A.546, V.547, D.548, R.571, H.574 Ligands: MN.8 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:I.442 Hydrogen bonds: B:Y.384, B:D.412, B:D.412, B:D.462, B:S.463, B:H.524, B:R.526, B:A.546, B:V.547, B:D.548, B:R.571 Water bridges: B:Q.460, B:D.462, B:R.571, B:H.574 Salt bridges: B:R.571, B:R.571, B:H.574

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 3 residues within 4Å: Chain A: D.184, H.329 Ligands: UDP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.184, A:H.329, H2O.7 MN.4: 4 residues within 4Å: Chain A: D.464, D.465, H.574 Ligands: UGA.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.464, A:D.464, A:H.574, H2O.5 MN.7: 3 residues within 4Å: Chain B: D.184, H.329 Ligands: UGA.5 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.184, B:H.329, H2O.12 MN.8: 3 residues within 4Å: Chain B: D.464, H.574 Ligands: UGA.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.464, B:D.464

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Osawa, T. et al., Crystal structure of chondroitin polymerase from Escherichia coli K4. Biochem. Biophys. Res. Commun. (2009)

Release Date

2008-09-16

Peptides

Chondroitin synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Chondroitin synthase

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