SMTL ID : 8u90.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

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

NA.1: 3 residues within 4Å: Chain A: H.12, D.48, T.83 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.12, A:T.83 NA.11: 3 residues within 4Å: Chain B: H.12, D.48, T.83 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.83, B:T.83 NA.21: 3 residues within 4Å: Chain C: H.12, D.48, T.83 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.48, C:T.83, C:T.83 NA.31: 3 residues within 4Å: Chain D: H.12, D.48, T.83 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.83, D:T.83, D:T.83

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

CL.2: 3 residues within 4Å: Chain A: A.59, Q.62, R.67 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain B: F.117 Ligands: CL.13 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: L.150 Chain B: L.150 Ligands: CL.14 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain B: A.59, Q.62, R.67 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain A: F.117 Ligands: CL.3 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain A: L.150 Chain B: L.150 Ligands: CL.4 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain C: A.59, Q.62, R.67 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain D: F.117 Ligands: CL.33 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain C: L.150 Chain D: L.150 Ligands: CL.34 Ligand excluded by PLIP CL.32: 3 residues within 4Å: Chain D: A.59, Q.62, R.67 Ligand excluded by PLIP CL.33: 2 residues within 4Å: Chain C: F.117 Ligands: CL.23 Ligand excluded by PLIP CL.34: 3 residues within 4Å: Chain C: L.150 Chain D: L.150 Ligands: CL.24 Ligand excluded by PLIP

8 x IOD: IODIDE ION(Non-functional Binders)

IOD.5: 1 residues within 4Å: Chain A: R.37 Ligand excluded by PLIP IOD.6: 7 residues within 4Å: Chain A: A.19, Y.51, G.54, S.55, T.56, Y.145, K.173 Ligand excluded by PLIP IOD.15: 1 residues within 4Å: Chain B: R.37 Ligand excluded by PLIP IOD.16: 7 residues within 4Å: Chain B: A.19, Y.51, G.54, S.55, T.56, Y.145, K.173 Ligand excluded by PLIP IOD.25: 1 residues within 4Å: Chain C: R.37 Ligand excluded by PLIP IOD.26: 7 residues within 4Å: Chain C: A.19, Y.51, G.54, S.55, T.56, Y.145, K.173 Ligand excluded by PLIP IOD.35: 1 residues within 4Å: Chain D: R.37 Ligand excluded by PLIP IOD.36: 7 residues within 4Å: Chain D: A.19, Y.51, G.54, S.55, T.56, Y.145, K.173 Ligand excluded by PLIP

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: D.178, Y.180 Chain C: G.177, Y.198, E.200 Ligand excluded by PLIP GOL.8: 7 residues within 4Å: Chain A: F.121, S.122, F.123, H.126, V.153, K.154, Q.159 Ligand excluded by PLIP GOL.9: 6 residues within 4Å: Chain A: R.32, R.36, E.69, E.72, I.73, E.76 Ligand excluded by PLIP GOL.10: 7 residues within 4Å: Chain A: L.206, G.209, A.210, D.211, L.232 Chain C: T.237, Q.241 Ligand excluded by PLIP GOL.17: 5 residues within 4Å: Chain B: D.178, Y.180 Chain D: G.177, Y.198, E.200 Ligand excluded by PLIP GOL.18: 7 residues within 4Å: Chain B: F.121, S.122, F.123, H.126, V.153, K.154, Q.159 Ligand excluded by PLIP GOL.19: 6 residues within 4Å: Chain B: R.32, R.36, E.69, E.72, I.73, E.76 Ligand excluded by PLIP GOL.20: 7 residues within 4Å: Chain B: L.206, G.209, A.210, D.211, L.232 Chain D: T.237, Q.241 Ligand excluded by PLIP GOL.27: 5 residues within 4Å: Chain A: G.177, Y.198, E.200 Chain C: D.178, Y.180 Ligand excluded by PLIP GOL.28: 7 residues within 4Å: Chain C: F.121, S.122, F.123, H.126, V.153, K.154, Q.159 Ligand excluded by PLIP GOL.29: 6 residues within 4Å: Chain C: R.32, R.36, E.69, E.72, I.73, E.76 Ligand excluded by PLIP GOL.30: 7 residues within 4Å: Chain A: T.237, Q.241 Chain C: L.206, G.209, A.210, D.211, L.232 Ligand excluded by PLIP GOL.37: 5 residues within 4Å: Chain B: G.177, Y.198, E.200 Chain D: D.178, Y.180 Ligand excluded by PLIP GOL.38: 7 residues within 4Å: Chain D: F.121, S.122, F.123, H.126, V.153, K.154, Q.159 Ligand excluded by PLIP GOL.39: 6 residues within 4Å: Chain D: R.32, R.36, E.69, E.72, I.73, E.76 Ligand excluded by PLIP GOL.40: 7 residues within 4Å: Chain B: T.237, Q.241 Chain D: L.206, G.209, A.210, D.211, L.232 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, hexagonal form). 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

Related Entries With Identical Sequence