SMTL ID : 6ckm.1

N. meningitidis CMP-sialic acid synthetase in the presence of CMP-sialic acid and Ca2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

homo-dimer

Ligands

2 x NCC: CYTIDINE-5'-MONOPHOSPHATE-5-N-ACETYLNEURAMINIC ACID(Non-covalent)

NCC.1: 17 residues within 4Å: Chain A: L.10, A.11, R.12, N.22, R.71, A.80, S.81, S.82, L.102, Q.104, P.105, T.106, N.175, G.176, Y.179, F.192 Ligands: CA.2 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:L.102, A:Y.179, A:F.192 Hydrogen bonds: A:R.12, A:R.12, A:N.22, A:R.71, A:R.71, A:A.80, A:S.82, A:S.82, A:Q.104, A:Q.104 Water bridges: A:S.82, A:S.82, A:T.106, A:T.106, A:R.173, A:P.174, A:Y.179 pi-Cation interactions: A:R.12 NCC.4: 17 residues within 4Å: Chain B: L.10, A.11, R.12, N.22, R.71, A.80, S.81, S.82, L.102, Q.104, P.105, T.106, N.175, G.176, Y.179, F.192 Ligands: CA.5 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:L.102, B:Y.179, B:F.192 Hydrogen bonds: B:R.12, B:R.12, B:N.22, B:R.71, B:R.71, B:A.80, B:S.82, B:S.82, B:Q.104, B:Q.104 Water bridges: B:S.82, B:S.82, B:T.106, B:T.106, B:R.173, B:P.174, B:D.209 pi-Cation interactions: B:R.12

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 2 residues within 4Å: Chain A: D.211 Ligands: NCC.1 No protein-ligand interaction detected (PLIP) CA.5: 2 residues within 4Å: Chain B: D.211 Ligands: NCC.4 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: D.46, R.47, I.48, G.65, E.67 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.46, A:I.48, A:E.67 GOL.6: 5 residues within 4Å: Chain B: D.46, R.47, I.48, G.65, E.67 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.46, B:I.48, B:E.67, B:E.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Matthews, M.M. et al., Catalytic Cycle ofNeisseria meningitidisCMP-Sialic Acid Synthetase Illustrated by High-Resolution Protein Crystallography. Biochemistry (2019)

Release Date

2019-03-06

Peptides

N-acylneuraminate cytidylyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

N-acylneuraminate cytidylyltransferase

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