SMTL ID : 2wqp.1

CRYSTAL STRUCTURE OF SIALIC ACID SYNTHASE NEUB-INHIBITOR COMPLEX

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x WQP: 5-(ACETYLAMINO)-3,5-DIDEOXY-2-O-PHOSPHONO-D-ERYTHRO-L-MANNO-NONONIC ACID(Non-covalent)

WQP.1: 24 residues within 4Å: Chain A: E.25, K.53, Q.55, N.74, M.83, T.110, F.112, K.129, G.131, S.132, S.154, C.182, N.184, Y.186, S.213, H.215, E.234, H.236, P.246, D.247 Chain B: T.285, A.289, R.314 Ligands: MN.2 20 PLIP interactions: 16 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Q.55, A:Q.55, A:N.74, A:S.132, A:S.154, A:N.184, A:Y.186, A:Y.186, A:S.213, A:S.213, A:D.247, B:R.314, B:R.314 Water bridges: A:I.28 Salt bridges: A:K.53, A:K.129, A:K.129, A:H.215 Hydrophobic interactions: B:T.285, B:A.289 WQP.9: 24 residues within 4Å: Chain A: T.285, A.289, R.314 Chain B: E.25, K.53, Q.55, N.74, M.83, T.110, F.112, K.129, G.131, S.132, S.154, C.182, N.184, Y.186, S.213, H.215, E.234, H.236, P.246, D.247 Ligands: MN.10 20 PLIP interactions: 16 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Q.55, B:Q.55, B:N.74, B:S.132, B:S.154, B:N.184, B:Y.186, B:Y.186, B:S.213, B:S.213, B:D.247, A:R.314, A:R.314 Water bridges: B:I.28 Salt bridges: B:K.53, B:K.129, B:K.129, B:H.215 Hydrophobic interactions: A:T.285, A:A.289

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

MN.2: 4 residues within 4Å: Chain A: H.215, E.234, H.236 Ligands: WQP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.215, A:H.236, H2O.312 MN.10: 4 residues within 4Å: Chain B: H.215, E.234, H.236 Ligands: WQP.9 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.215, B:H.236, H2O.634

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 8 residues within 4Å: Chain A: Q.2, M.198, N.199, S.202, I.210, L.228, G.229, G.230 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.2, A:I.210 Hydrogen bonds: A:S.202, A:G.229 ACT.11: 8 residues within 4Å: Chain B: Q.2, M.198, N.199, S.202, I.210, L.228, G.229, G.230 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Q.2, B:I.210 Hydrogen bonds: B:S.202, B:G.229

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 5 residues within 4Å: Chain A: T.188, P.189, Y.190, T.216, L.217 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.217 Water bridges: A:Y.190 EDO.5: 9 residues within 4Å: Chain A: K.275, D.276, T.277, I.278, K.286 Chain B: M.157, N.158, S.159, R.194 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:K.275, A:K.286, B:R.194 Water bridges: A:I.279, B:S.159, B:R.194 EDO.6: 3 residues within 4Å: Chain A: D.218, N.219, Y.220 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:Q.262, A:E.259 Hydrogen bonds: A:N.219, A:N.219 EDO.7: 5 residues within 4Å: Chain A: I.71, P.72, G.73, A.75, D.76 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.75 EDO.12: 5 residues within 4Å: Chain B: T.188, P.189, Y.190, T.216, L.217 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.217 Water bridges: B:Y.190 EDO.13: 9 residues within 4Å: Chain A: M.157, N.158, S.159, R.194 Chain B: K.275, D.276, T.277, I.278, K.286 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:K.275, B:K.286, A:R.194 Water bridges: B:I.279, A:S.159, A:R.194 EDO.14: 3 residues within 4Å: Chain B: D.218, N.219, Y.220 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.219, B:N.219 Water bridges: B:E.259, A:Q.262 EDO.15: 5 residues within 4Å: Chain B: I.71, P.72, G.73, A.75, D.76 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.75

2 x LMR: (2S)-2-HYDROXYBUTANEDIOIC ACID(Non-covalent)

LMR.8: 3 residues within 4Å: Chain A: H.265, L.269 Chain B: Y.190 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.269 Salt bridges: A:H.265 LMR.16: 3 residues within 4Å: Chain A: Y.190 Chain B: H.265, L.269 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.269 Salt bridges: B:H.265

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, F. et al., The Inhibition of Neisseria Meningitidis Sialic Acid Synthase by a Tetrahedral Intermediate Analog. Biochemistry (2009)

Release Date

2009-09-15

Peptides

POLYSIALIC ACID CAPSULE BIOSYNTHESIS PROTEIN SIAC: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

POLYSIALIC ACID CAPSULE BIOSYNTHESIS PROTEIN SIAC