SMTL ID : 4imf.1

Crystal Structure of Pasteurella multocida N-Acetyl-D-Neuraminic acid lyase K164 mutant complexed with N-Acetylneuraminic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

4 x SI3: 5-(acetylamino)-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosonic acid(Non-covalent)

SI3.1: 17 residues within 4Å: Chain A: A.10, G.46, S.47, T.48, Y.136, I.138, F.140, T.166, G.188, F.189, D.190, E.191, I.205, G.206, S.207, L.250, Y.251 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:A.10, A:I.138, A:F.140, A:I.205 Hydrogen bonds: A:T.48, A:T.166, A:G.188, A:G.188, A:D.190, A:I.205, A:S.207, A:S.207 Water bridges: A:G.46 SI3.7: 17 residues within 4Å: Chain B: A.10, G.46, S.47, T.48, Y.136, I.138, F.140, T.166, G.188, F.189, D.190, E.191, I.205, G.206, S.207, L.250, Y.251 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:A.10, B:I.138, B:F.140, B:I.205 Hydrogen bonds: B:T.48, B:T.48, B:G.188, B:D.190, B:I.205, B:S.207, B:S.207, B:Y.251 Water bridges: B:G.46 SI3.11: 17 residues within 4Å: Chain C: A.10, G.46, S.47, T.48, Y.136, I.138, F.140, T.166, G.188, F.189, D.190, E.191, I.205, G.206, S.207, L.250, Y.251 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:A.10, C:I.138, C:F.140, C:I.205 Hydrogen bonds: C:T.48, C:T.48, C:Y.136, C:G.188, C:G.188, C:D.190, C:I.205, C:S.207, C:S.207, C:Y.251 Water bridges: C:G.46 SI3.17: 17 residues within 4Å: Chain D: A.10, G.46, S.47, T.48, Y.136, I.138, F.140, T.166, G.188, F.189, D.190, E.191, I.205, G.206, S.207, L.250, Y.251 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:A.10, D:I.138, D:F.140, D:I.205 Hydrogen bonds: D:T.48, D:Y.136, D:T.166, D:G.188, D:D.190, D:I.205, D:S.207, D:S.207 Water bridges: D:G.46

6 x ME2: 1-ETHOXY-2-(2-METHOXYETHOXY)ETHANE(Non-covalent)

ME2.2: 6 residues within 4Å: Chain A: G.147, D.169, Y.171, L.172, R.175 Chain C: E.243 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.169, A:Y.171 ME2.8: 10 residues within 4Å: Chain A: P.139, F.140, L.141, T.142, G.143 Chain B: P.139, F.140, L.141, T.142, G.143 No protein-ligand interaction detected (PLIP) ME2.9: 7 residues within 4Å: Chain B: G.147, V.148, D.169, Y.171, L.172, R.175 Chain D: E.243 No protein-ligand interaction detected (PLIP) ME2.12: 6 residues within 4Å: Chain A: E.243 Chain C: G.147, D.169, Y.171, L.172, R.175 No protein-ligand interaction detected (PLIP) ME2.18: 10 residues within 4Å: Chain C: P.139, F.140, L.141, T.142, G.143 Chain D: P.139, F.140, L.141, T.142, G.143 No protein-ligand interaction detected (PLIP) ME2.19: 7 residues within 4Å: Chain B: E.243 Chain D: G.147, V.148, D.169, Y.171, L.172, R.175 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Water bridges: D:D.169, D:Y.171, B:E.243

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

CL.3: 1 residues within 4Å: Chain A: G.168 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: Y.180, N.182, H.183 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: Y.180, P.181, N.182, H.183 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain C: G.168 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain C: Y.180, N.182, H.183 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain D: Y.180, P.181, N.182, H.183 Ligand excluded by PLIP

4 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.5: 2 residues within 4Å: Chain A: F.113, Q.150 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.150, A:Q.150 Water bridges: A:F.115 IPA.6: 4 residues within 4Å: Chain A: P.158, V.160, L.161, N.182 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.161 IPA.15: 2 residues within 4Å: Chain C: F.113, Q.150 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.150, C:Q.150 Water bridges: C:F.115 IPA.16: 4 residues within 4Å: Chain C: P.158, V.160, L.161, N.182 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huynh, N. et al., Structural Basis for Substrate Specificity and Mechanism of N-Acetyl-d-neuraminic Acid Lyase from Pasteurella multocida. Biochemistry (2013)

Release Date

2013-11-06

Peptides

N-acetylneuraminate lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

N-acetylneuraminate lyase

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