SMTL ID : 8u93.1

Crystal structure of N-acetylneuraminate lyase (NanA) from Klebsiella aerogenes (PEG bound)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

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

CL.1: 1 residues within 4Å: Chain A: R.105 Ligand excluded by PLIP CL.2: 1 residues within 4Å: Chain A: R.37 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain B: R.105 Ligand excluded by PLIP CL.9: 1 residues within 4Å: Chain B: R.37 Ligand excluded by PLIP CL.15: 1 residues within 4Å: Chain C: R.105 Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain C: R.37 Ligand excluded by PLIP CL.22: 1 residues within 4Å: Chain D: R.105 Ligand excluded by PLIP CL.23: 1 residues within 4Å: Chain D: R.37 Ligand excluded by PLIP

4 x K: POTASSIUM ION(Non-functional Binders)

K.3: 1 residues within 4Å: Ligands: 1PG.7 No protein-ligand interaction detected (PLIP) K.10: 1 residues within 4Å: Ligands: 1PG.14 No protein-ligand interaction detected (PLIP) K.17: 1 residues within 4Å: Ligands: 1PG.21 No protein-ligand interaction detected (PLIP) K.24: 1 residues within 4Å: Ligands: 1PG.28 No protein-ligand interaction detected (PLIP)

4 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.4: 6 residues within 4Å: Chain A: G.152, K.154 Chain B: A.149, G.152, K.154 Ligands: DTT.11 No protein-ligand interaction detected (PLIP) DTT.11: 6 residues within 4Å: Chain A: A.149, G.152, K.154 Chain B: G.152, K.154 Ligands: DTT.4 No protein-ligand interaction detected (PLIP) DTT.18: 6 residues within 4Å: Chain C: G.152, K.154 Chain D: A.149, G.152, K.154 Ligands: DTT.25 No protein-ligand interaction detected (PLIP) DTT.25: 6 residues within 4Å: Chain C: A.149, G.152, K.154 Chain D: G.152, K.154 Ligands: DTT.18 No protein-ligand interaction detected (PLIP)

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 8 residues within 4Å: Chain A: V.255, K.256, V.257, G.258, R.261 Chain B: P.120, F.121, S.122 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:S.122, A:R.261, A:R.261 Hydrogen bonds: A:R.261 PEG.12: 8 residues within 4Å: Chain A: P.120, F.121, S.122 Chain B: V.255, K.256, V.257, G.258, R.261 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Water bridges: A:S.122, B:R.261, B:R.261 Hydrogen bonds: B:R.261 PEG.19: 8 residues within 4Å: Chain C: V.255, K.256, V.257, G.258, R.261 Chain D: P.120, F.121, S.122 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Water bridges: D:S.122, C:R.261, C:R.261 Hydrogen bonds: C:R.261 PEG.26: 8 residues within 4Å: Chain C: P.120, F.121, S.122 Chain D: V.255, K.256, V.257, G.258, R.261 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Water bridges: C:S.122, D:R.261, D:R.261 Hydrogen bonds: D:R.261

8 x 1PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL(Non-covalent)

1PG.6: 5 residues within 4Å: Chain A: R.32, R.36, E.69, E.72, E.76 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.32, A:R.32, A:R.36 1PG.7: 9 residues within 4Å: Chain A: A.149, L.150, Y.198, D.199, E.200, S.216, I.251, V.255 Ligands: K.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.199, A:D.199 1PG.13: 5 residues within 4Å: Chain B: R.32, R.36, E.69, E.72, E.76 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.32, B:R.32, B:R.36 1PG.14: 9 residues within 4Å: Chain B: A.149, L.150, Y.198, D.199, E.200, S.216, I.251, V.255 Ligands: K.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.199, B:D.199 1PG.20: 5 residues within 4Å: Chain C: R.32, R.36, E.69, E.72, E.76 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.32, C:R.32, C:R.36 1PG.21: 9 residues within 4Å: Chain C: A.149, L.150, Y.198, D.199, E.200, S.216, I.251, V.255 Ligands: K.17 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.199, C:D.199 Water bridges: C:E.200 1PG.27: 5 residues within 4Å: Chain D: R.32, R.36, E.69, E.72, E.76 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.32, D:R.32, D:R.36 1PG.28: 9 residues within 4Å: Chain D: A.149, L.150, Y.198, D.199, E.200, S.216, I.251, V.255 Ligands: K.24 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.199, D:D.199 Water bridges: D:E.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lovell, S. et al., Crystal structure of N-acetylneuraminate lyase (NanA) from Klebsiella aerogenes (PEG bound). To be published

Release Date

2023-09-27

Peptides

N-acetylneuraminate lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

N-acetylneuraminate lyase

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