SMTL ID : 2yk5.1

Structure of Neisseria LOS-specific sialyltransferase (NST), in complex with CMP.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

homo-dimer

Ligands

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

C.1: 15 residues within 4Å: Chain A: L.206, G.207, A.230, P.231, H.232, P.233, V.250, I.251, E.252, S.274, G.275, A.276 Chain B: L.11, F.70 Ligands: PO4.2 24 PLIP interactions: 12 interactions with chain A, 12 interactions with chain B Hydrogen bonds: A:A.230, A:I.251, A:E.252, A:G.275, A:T.279, B:A.230, B:I.251, B:E.252, B:G.275, B:T.279 Water bridges: A:I.71, A:T.119, A:H.232, A:H.232, A:R.234, A:G.275, B:I.71, B:T.119, B:H.232, B:H.232, B:R.234, B:G.275 Salt bridges: A:H.232, B:H.232 C.9: 15 residues within 4Å: Chain A: L.11, F.70 Chain B: L.206, G.207, A.230, P.231, H.232, P.233, V.250, I.251, E.252, S.274, G.275, A.276 Ligands: PO4.10 Protein-ligand interaction information (PLIP) not available

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 5 residues within 4Å: Chain A: H.232, R.234 Chain B: N.69, F.70 Ligands: C.1 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B Salt bridges: A:H.232, A:R.234 Hydrogen bonds: B:N.69 Water bridges: B:I.10, B:I.10, B:I.10, B:Y.41, B:Y.41 PO4.10: 5 residues within 4Å: Chain A: N.69, F.70 Chain B: H.232, R.234 Ligands: C.9 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain A Salt bridges: B:H.232, B:R.234 Hydrogen bonds: A:N.69 Water bridges: A:I.10, A:I.10, A:I.10, A:Y.41, A:Y.41

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.3: 10 residues within 4Å: Chain A: Y.8, N.65, S.67, A.102, T.106 Chain B: L.95, E.96, V.98, S.99, I.100 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.99, A:S.67 Water bridges: A:S.67 1PE.11: 10 residues within 4Å: Chain A: L.95, E.96, V.98, S.99, I.100 Chain B: Y.8, N.65, S.67, A.102, T.106 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.99, B:S.67 Water bridges: B:S.67

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 2 residues within 4Å: Chain A: N.38, E.39 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.39 SO4.5: 2 residues within 4Å: Chain A: R.203, N.225 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.225 Salt bridges: A:R.203 SO4.6: 4 residues within 4Å: Chain A: G.130, D.131, E.132, K.303 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.131, A:E.132 Salt bridges: A:K.303 SO4.12: 2 residues within 4Å: Chain B: N.38, E.39 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.39 SO4.13: 2 residues within 4Å: Chain B: R.203, N.225 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.225 Salt bridges: B:R.203 SO4.14: 4 residues within 4Å: Chain B: G.130, D.131, E.132, K.303 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.131, B:E.132 Salt bridges: B:K.303

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

EDO.7: 7 residues within 4Å: Chain A: D.116, D.117, G.118, I.166 Chain B: L.11, Q.12, V.15 No protein-ligand interaction detected (PLIP) EDO.8: 8 residues within 4Å: Chain A: A.230, P.231, L.245, Y.249, V.250, I.251, Y.254 Chain B: K.40 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:K.40, A:L.245, A:V.250 Water bridges: A:S.247, A:I.251 EDO.15: 7 residues within 4Å: Chain A: L.11, Q.12, V.15 Chain B: D.116, D.117, G.118, I.166 No protein-ligand interaction detected (PLIP) EDO.16: 8 residues within 4Å: Chain A: K.40 Chain B: A.230, P.231, L.245, Y.249, V.250, I.251, Y.254 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.245, B:V.250, A:K.40 Water bridges: B:S.247, B:I.251

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, L.Y.C. et al., Structure and Mechanism of the Lipooligosaccharide Sialyltransferase from Neisseria Meningitidis. J.Biol.Chem. (2011)

Release Date

2011-08-31

Peptides

CMP-N-ACETYLNEURAMINATE-BETA-GALACTOSAMIDE-ALPHA-2,3-SIALYLTRANSFERASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

CMP-N-ACETYLNEURAMINATE-BETA-GALACTOSAMIDE-ALPHA-2,3-SIALYLTRANSFERASE

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