SMTL ID : 6ckl.1 (1 other biounit)

N. meningitidis CMP-sialic acid synthetase in the presence of CMP and Neu5Ac2en

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.68 Å

Oligo State

homo-dimer

Ligands

2 x C5P: CYTIDINE-5'-MONOPHOSPHATE(Non-covalent)

C5P.1: 15 residues within 4Å: Chain A: L.10, A.11, R.12, N.22, R.71, L.75, A.80, S.81, S.82, Q.104, P.105, T.106 Chain B: R.165 Ligands: CL.2, DAN.4 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.12, A:R.12, A:R.12, A:N.22, A:R.71, A:R.71, A:L.75 Salt bridges: A:K.21, B:R.165 pi-Cation interactions: A:R.12 C5P.6: 15 residues within 4Å: Chain A: R.165 Chain B: L.10, A.11, R.12, N.22, R.71, L.75, A.80, S.81, S.82, Q.104, P.105, T.106 Ligands: DAN.3, CL.7 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.12, B:R.12, B:N.22, B:R.71, B:R.71, B:L.75, B:T.106 Salt bridges: B:K.21, A:R.165 pi-Cation interactions: B:R.12

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 4 residues within 4Å: Chain A: R.12, S.15, K.21 Ligands: C5P.1 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain B: R.12, S.15, K.21 Ligands: C5P.6 Ligand excluded by PLIP

2 x DAN: 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID(Non-covalent)

DAN.3: 15 residues within 4Å: Chain A: K.142, L.161, E.162, P.164, R.165 Chain B: S.81, S.82, L.102, Q.104, P.174, N.175, G.176, Y.179, F.192 Ligands: C5P.6 14 PLIP interactions: 5 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:K.142, A:L.161, A:R.165, B:S.82, B:S.82, B:S.82, B:Q.104, B:P.174, B:Y.179 Salt bridges: A:K.142, A:R.165 Hydrophobic interactions: B:L.102, B:Y.179, B:F.192 DAN.4: 14 residues within 4Å: Chain A: S.81, S.82, L.102, Q.104, N.175, Y.179, F.192 Chain B: K.142, L.161, E.162, Q.163, P.164, R.165 Ligands: C5P.1 17 PLIP interactions: 12 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:L.102, A:Y.179, A:F.192 Hydrogen bonds: A:A.80, A:S.82, A:S.82, A:S.82, A:Q.104, A:P.174, A:Y.179, B:K.142, B:L.161, B:R.165 Water bridges: A:T.106, A:D.209 Salt bridges: B:K.142, B:R.165

1 x FLC: CITRATE ANION(Non-covalent)

FLC.5: 10 residues within 4Å: Chain A: M.136, E.137, H.138, R.173, H.204 Chain B: M.136, E.137, H.138, R.173, H.204 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:E.137, A:H.138, A:H.138, A:R.173, B:E.137 Salt bridges: A:H.138, A:H.204, B:R.173, B:H.204, B:H.204

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
B

N-acylneuraminate cytidylyltransferase

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