SMTL ID : 3k8d.2 (1 other biounit)

Crystal structure of E. coli lipopolysaccharide specific CMP-KDO synthetase in complex with CTP and 2-deoxy-Kdo

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain B: R.180 Ligands: CTP.3 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain A: R.180 Ligands: CTP.6 No protein-ligand interaction detected (PLIP)

2 x KDO: 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid(Non-covalent)

KDO.2: 13 residues within 4Å: Chain A: R.31, Q.114, V.158, R.173, H.197, G.199, Y.201, M.224, L.225, E.226, Q.227, D.251 Ligands: CTP.3 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:Q.114, A:H.197, A:H.197, A:Y.201, A:Y.201, A:M.224, A:E.226, A:E.226, A:E.226, A:Q.227 Water bridges: A:R.31, A:R.31, A:V.158, A:R.173, A:G.199, A:D.251, A:D.251 Salt bridges: A:R.31, A:R.173 KDO.5: 13 residues within 4Å: Chain B: R.31, Q.114, V.158, R.173, H.197, G.199, Y.201, M.224, L.225, E.226, Q.227, D.251 Ligands: CTP.6 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:Q.114, B:H.197, B:H.197, B:Y.201, B:Y.201, B:M.224, B:E.226, B:E.226, B:E.226, B:Q.227 Water bridges: B:R.31, B:R.31, B:N.156, B:R.173, B:G.199, B:G.199, B:D.251 Salt bridges: B:R.31, B:R.173

2 x CTP: CYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

CTP.3: 19 residues within 4Å: Chain A: P.24, A.25, R.26, S.29, T.30, R.31, K.35, H.88, Q.89, S.90, G.91, R.94, Q.114, G.115, D.116, D.251 Chain B: R.180 Ligands: MG.1, KDO.2 24 PLIP interactions: 23 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.26, A:R.26, A:T.30, A:R.31, A:H.88, A:G.91, A:R.94, A:G.115, A:D.116, A:D.116 Water bridges: A:R.26, A:R.26, A:L.32, A:L.32, A:T.92, A:G.115 Salt bridges: A:R.26, A:R.26, A:R.31, A:R.31, A:K.35, A:K.35, A:K.35, B:R.180 CTP.6: 19 residues within 4Å: Chain A: R.180 Chain B: P.24, A.25, R.26, S.29, T.30, R.31, K.35, H.88, Q.89, S.90, G.91, R.94, Q.114, G.115, D.116, D.251 Ligands: MG.4, KDO.5 24 PLIP interactions: 22 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.26, B:R.26, B:T.30, B:R.31, B:R.31, B:H.88, B:G.91, B:R.94, B:G.115, B:D.116, B:D.116 Water bridges: B:R.26, B:L.32, B:L.32, B:Q.114, B:G.115, A:R.180 Salt bridges: B:R.26, B:R.26, B:R.31, B:K.35, B:K.35, B:K.35, A:R.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Heyes, D.J. et al., Structure-based mechanism of CMP-2-keto-3-deoxymanno-octulonic acid synthetase: convergent evolution of a sugar-activating enzyme with DNA/RNA polymerases. J.Biol.Chem. (2009)

Release Date

2009-11-10

Peptides

3-deoxy-manno-octulosonate cytidylyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

3-deoxy-manno-octulosonate cytidylyltransferase

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