SMTL ID : 2z87.1 (2 other biounits)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-dimer

Ligands

2 x UD2: URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE(Non-covalent)

UD2.1: 21 residues within 4Å: Chain A: P.99, T.100, Y.101, R.103, D.130, G.158, Y.159, L.161, V.164, R.165, D.181, C.182, D.183, M.184, R.210, S.276, G.278, E.303, D.304, H.328 Ligands: MN.3 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.101 Hydrogen bonds: A:P.99, A:Y.101, A:D.130, A:R.165, A:D.181, A:D.181, A:C.182, A:E.303, A:D.304 Water bridges: A:R.210, A:G.278, A:G.278 Salt bridges: A:R.103 pi-Stacking: A:Y.159 UD2.5: 21 residues within 4Å: Chain B: P.99, T.100, Y.101, R.103, D.130, G.158, Y.159, L.161, V.164, R.165, D.181, C.182, D.183, M.184, H.299, W.300, G.301, E.303, D.304, H.328 Ligands: MN.7 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.101 Hydrogen bonds: B:P.99, B:D.130, B:R.165, B:D.181, B:D.181, B:D.181, B:C.182, B:G.301, B:D.304 Water bridges: B:R.103, B:R.103 Salt bridges: B:R.103 pi-Stacking: B:Y.159

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

UDP.2: 14 residues within 4Å: Chain A: P.381, A.382, Y.383, D.411, N.438, G.440, I.441, A.444, D.461, S.462, D.463, R.570, H.573 Ligands: MN.4 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.383, A:I.441 Hydrogen bonds: A:Y.383, A:Y.383, A:D.411, A:D.411, A:N.438, A:G.440, A:S.462, A:S.462, A:S.462, A:D.463, A:R.570 Salt bridges: A:H.573, A:H.573 UDP.6: 13 residues within 4Å: Chain B: P.381, A.382, Y.383, D.411, N.438, G.440, I.441, A.444, D.461, S.462, D.463, H.573 Ligands: MN.8 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.383, B:I.441 Hydrogen bonds: B:Y.383, B:D.411, B:D.411, B:S.462, B:S.462, B:S.462 Water bridges: B:D.461, B:D.461 Salt bridges: B:H.573, B:H.573

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

MN.3: 4 residues within 4Å: Chain A: R.103, D.183, H.328 Ligands: UD2.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.183, A:H.328, H2O.1 MN.4: 4 residues within 4Å: Chain A: D.463, D.464, H.573 Ligands: UDP.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.463, A:D.463, A:H.573 MN.7: 4 residues within 4Å: Chain B: R.103, D.183, H.328 Ligands: UD2.5 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.183, B:H.328, H2O.5, H2O.6 MN.8: 3 residues within 4Å: Chain B: D.463, H.573 Ligands: UDP.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.463, B:D.463

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
A

B
B

Chondroitin synthase

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