SMTL ID : 8u92.2 (1 other biounit)

Crystal structure of N-acetylneuraminate lyase (NanA) from Klebsiella aerogenes (pyruvate bound, Orthorhombic P form)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

8 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 8 residues within 4Å: Chain A: Y.198, D.199, E.200, S.216, T.217, I.251, V.255 Ligands: GOL.9 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.217, A:I.251, A:V.255 Hydrogen bonds: A:D.199 Water bridges: A:G.197, A:D.199, A:E.200 MPD.2: 6 residues within 4Å: Chain A: D.178, Y.180 Chain B: G.177, Y.198, E.200, I.201 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Y.198, B:E.200, B:I.201, A:Y.180 Water bridges: B:G.177, A:G.177, A:L.179 MPD.10: 5 residues within 4Å: Chain A: G.177, Y.198, E.200, I.201 Chain B: D.178 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.198, A:Y.198, A:E.200, A:I.201 Water bridges: B:L.179 MPD.11: 6 residues within 4Å: Chain B: Y.198, D.199, E.200, S.216, I.251, V.255 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.251, B:V.255 Hydrogen bonds: B:D.199 Water bridges: B:G.197, B:D.199, B:D.199 MPD.20: 8 residues within 4Å: Chain C: Y.198, D.199, E.200, S.216, T.217, I.251, V.255 Ligands: GOL.28 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:T.217, C:I.251, C:V.255 Hydrogen bonds: C:D.199 Water bridges: C:G.197, C:D.199, C:E.200 MPD.21: 6 residues within 4Å: Chain C: D.178, Y.180 Chain D: G.177, Y.198, E.200, I.201 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:Y.198, D:E.200, D:I.201, C:Y.180 Water bridges: D:G.177, C:G.177, C:L.179 MPD.29: 5 residues within 4Å: Chain C: G.177, Y.198, E.200, I.201 Chain D: D.178 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:Y.198, C:Y.198, C:E.200, C:I.201 Water bridges: D:L.179 MPD.30: 6 residues within 4Å: Chain D: Y.198, D.199, E.200, S.216, I.251, V.255 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:I.251, D:V.255 Hydrogen bonds: D:D.199 Water bridges: D:G.197, D:D.199, D:D.199

4 x NA: SODIUM ION(Non-functional Binders)

NA.3: 3 residues within 4Å: Chain A: H.12, D.48, T.83 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.83, A:T.83, A:T.83 NA.12: 3 residues within 4Å: Chain B: H.12, D.48, T.83 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.12, B:T.83 NA.22: 3 residues within 4Å: Chain C: H.12, D.48, T.83 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.12, C:T.83, C:T.83 NA.31: 3 residues within 4Å: Chain D: H.12, D.48, T.83 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.48, D:T.83

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

CL.4: 1 residues within 4Å: Chain A: F.121 Ligand excluded by PLIP CL.5: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.6: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain A: M.270 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain B: R.32, R.36 Ligand excluded by PLIP CL.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.15: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.16: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.17: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.18: 1 residues within 4Å: Ligands: CL.37 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain B: R.105, Y.106 Ligand excluded by PLIP CL.23: 1 residues within 4Å: Chain C: F.121 Ligand excluded by PLIP CL.24: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.25: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.26: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.27: 1 residues within 4Å: Chain C: M.270 Ligand excluded by PLIP CL.32: 2 residues within 4Å: Chain D: R.32, R.36 Ligand excluded by PLIP CL.33: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.34: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.35: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.36: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.37: 1 residues within 4Å: Ligands: CL.18 Ligand excluded by PLIP CL.38: 2 residues within 4Å: Chain D: R.105, Y.106 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 7 residues within 4Å: Chain A: T.56, L.150, K.173, T.175, G.197, Y.198 Ligands: MPD.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.56, A:T.56, A:G.197 Water bridges: A:Y.198 GOL.28: 7 residues within 4Å: Chain C: T.56, L.150, K.173, T.175, G.197, Y.198 Ligands: MPD.20 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.56, C:T.56, C:G.197 Water bridges: C:Y.198

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2023-09-27

Peptides

N-acetylneuraminate lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
E

D
F

N-acetylneuraminate lyase

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