SMTL ID : 8u91.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-tetramer

Ligands

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

MPD.1: 6 residues within 4Å: Chain A: Y.198, D.199, E.200, T.217, I.251, V.255 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.217, A:I.251, A:V.255 Hydrogen bonds: A:D.199 MPD.5: 4 residues within 4Å: Chain A: Y.198, E.200, I.201 Chain B: D.178 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.198, A:Y.198, A:E.200, A:I.201 MPD.6: 5 residues within 4Å: Chain B: Y.198, D.199, E.200, S.216, V.255 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.255 Hydrogen bonds: B:D.199 Water bridges: B:D.199, B:S.216 MPD.7: 5 residues within 4Å: Chain A: D.178 Chain B: G.177, Y.198, E.200, I.201 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.198, B:Y.198, B:E.200, B:I.201 Water bridges: A:D.178 MPD.14: 6 residues within 4Å: Chain C: Y.198, D.199, E.200, T.217, I.251, V.255 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:T.217, C:I.251, C:V.255 Hydrogen bonds: C:D.199 MPD.18: 4 residues within 4Å: Chain C: Y.198, E.200, I.201 Chain D: D.178 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.198, C:Y.198, C:E.200, C:I.201 MPD.19: 5 residues within 4Å: Chain D: Y.198, D.199, E.200, S.216, V.255 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:V.255 Hydrogen bonds: D:D.199 Water bridges: D:D.199, D:S.216 MPD.20: 5 residues within 4Å: Chain C: D.178 Chain D: G.177, Y.198, E.200, I.201 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:Y.198, D:Y.198, D:E.200, D:I.201 Water bridges: C:D.178

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

CL.2: 6 residues within 4Å: Chain A: Y.51, G.54, S.55, T.56, Y.145, K.173 Ligand excluded by PLIP CL.3: 1 residues within 4Å: Chain A: M.270 Ligand excluded by PLIP CL.4: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.9: 1 residues within 4Å: Chain B: S.274 Ligand excluded by PLIP CL.10: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.11: 7 residues within 4Å: Chain B: A.19, Y.51, G.54, S.55, T.56, Y.145, K.173 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain B: R.105, Y.106 Ligand excluded by PLIP CL.13: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.15: 6 residues within 4Å: Chain C: Y.51, G.54, S.55, T.56, Y.145, K.173 Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain C: M.270 Ligand excluded by PLIP CL.17: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.21: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.22: 1 residues within 4Å: Chain D: S.274 Ligand excluded by PLIP CL.23: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.24: 7 residues within 4Å: Chain D: A.19, Y.51, G.54, S.55, T.56, Y.145, K.173 Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain D: R.105, Y.106 Ligand excluded by PLIP CL.26: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lovell, S. et al., Crystal structure of N-acetylneuraminate lyase (NanA) from Klebsiella aerogenes (Apo, 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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