SMTL ID : 7a5x.1

Two copies of the catalytic domain of NanA sialidase from Streptococcus pneumoniae juxtaposed in the P212121 space group, in complex with DANA derivatized with a PEG linker on the glycerol group.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-dimer

Ligands

2 x R7H: (4~{S},5~{R},6~{R})-5-acetamido-6-[(1~{R},2~{S})-3-[[1-(2-ethoxyethyl)-1,2,3-triazol-4-yl]methylsulfanyl]-1,2-bis(oxidanyl)propyl]-4-oxidanyl-oxane-2-carboxylic acid(Non-covalent)

R7H.1: 22 residues within 4Å: Chain A: R.54, I.55, R.73, D.79, I.123, D.124, D.141, F.143, I.149, F.150, F.272, Y.297, L.305, N.306, Q.309, R.348, T.353, E.354, R.370, Y.402, R.428, Y.459 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:R.73, A:D.79, A:D.124, A:R.348 Water bridges: A:Y.297, A:Y.297, A:Q.309, A:R.428 Salt bridges: A:R.54, A:R.370, A:R.428 R7H.5: 23 residues within 4Å: Chain B: R.54, I.55, R.73, D.79, I.123, D.124, D.141, F.143, I.149, F.150, F.272, P.277, Y.297, L.305, N.306, Q.309, R.348, T.353, E.354, R.370, Y.402, R.428, Y.459 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:I.55 Hydrogen bonds: B:R.73, B:D.124, B:D.124, B:Y.297 Water bridges: B:R.54, B:I.149, B:Q.309, B:Q.309, B:Q.309, B:R.370, B:R.428 Salt bridges: B:R.54, B:R.370, B:R.428

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

SO4.2: 5 residues within 4Å: Chain A: K.33, Q.453, K.454, E.478, R.489 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.453 Water bridges: A:R.489 Salt bridges: A:R.489 SO4.6: 4 residues within 4Å: Chain B: K.33, Q.453, E.478, R.489 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.453 Water bridges: B:K.33, B:K.33, B:H.476, B:R.489, B:R.489 Salt bridges: B:R.489

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

CL.3: 6 residues within 4Å: Chain A: G.223, N.224, F.227, K.231, T.232, S.233 Ligand excluded by PLIP CL.7: 6 residues within 4Å: Chain B: G.223, N.224, F.227, K.231, T.232, S.233 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain B: N.285, G.286, K.289 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain B: D.99, R.100 Ligand excluded by PLIP

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 7 residues within 4Å: Chain A: D.82, I.83, N.105, L.106, R.107, D.108, S.119 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.82, A:L.106, A:S.119 CA.10: 7 residues within 4Å: Chain B: D.82, I.83, N.105, L.106, R.107, D.108, S.119 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.82, B:L.106, B:D.108, H2O.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Assailly, C. et al., Polyvalent Transition-State Analogues of Sialyl Substrates Strongly Inhibit Bacterial Sialidases*. Chemistry (2021)

Release Date

2020-11-18

Peptides

Sialidase A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Sialidase A

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