SMTL ID : 4imc.1

Crystal Structure of Pasteurella multocida N-Acetyl-D-Neuraminic acid lyase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

7 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 5 residues within 4Å: Chain A: A.179, Y.180, P.181, N.182, H.183 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.179, A:Y.180, A:N.182, A:N.182, A:H.183 Salt bridges: A:H.183 PO4.2: 3 residues within 4Å: Chain A: K.119, H.120, D.123 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.123 Water bridges: A:H.120, A:H.120 Salt bridges: A:H.120 PO4.7: 5 residues within 4Å: Chain B: A.179, Y.180, P.181, N.182, H.183 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.182, B:N.182, B:H.183 Salt bridges: B:H.183 PO4.8: 3 residues within 4Å: Chain B: K.119, H.120, D.123 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.123, B:D.123, B:D.123 Water bridges: B:H.120, B:H.120 Salt bridges: B:H.120 PO4.13: 4 residues within 4Å: Chain C: Y.180, P.181, N.182, H.183 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.182, C:N.182, C:H.183 Salt bridges: C:H.183 PO4.18: 4 residues within 4Å: Chain D: Y.180, P.181, N.182, H.183 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Y.180, D:N.182, D:N.182, D:H.183 Salt bridges: D:H.183 PO4.19: 3 residues within 4Å: Chain D: K.119, H.120, D.123 4 PLIP interactions: 4 interactions with chain D Water bridges: D:H.120, D:H.120 Salt bridges: D:K.119, D:H.120

14 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 8 residues within 4Å: Chain A: A.10, Y.43, G.46, S.47, T.48, Y.136, K.164, I.205 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.47, A:T.48, A:K.164, A:K.164 Water bridges: A:S.207 EDO.4: 7 residues within 4Å: Chain A: F.189, D.190, E.191, T.208, I.242, L.246, L.250 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.190, A:D.190 Water bridges: A:S.207, A:S.207 EDO.5: 4 residues within 4Å: Chain A: P.158, L.161, N.182, H.183 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.161 EDO.6: 7 residues within 4Å: Chain A: F.165, A.167, F.170, A.187, G.188, F.189, A.196 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.188, A:F.189 EDO.9: 8 residues within 4Å: Chain B: A.10, G.46, S.47, T.48, Y.136, I.138, K.164, T.166 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.47, B:T.48, B:K.164, B:T.166 EDO.10: 6 residues within 4Å: Chain B: G.188, F.189, D.190, E.191, T.208, L.250 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.190, B:D.190 Water bridges: B:S.207, B:S.207 EDO.11: 7 residues within 4Å: Chain B: F.165, A.167, F.170, A.187, G.188, F.189, A.196 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.188, B:F.189, B:F.189 EDO.12: 4 residues within 4Å: Chain B: V.160, L.161, N.182, H.183 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.182 Water bridges: B:P.158, B:V.160 EDO.14: 7 residues within 4Å: Chain C: A.10, Y.43, G.46, S.47, T.48, Y.136, K.164 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:T.48, C:T.48, C:Y.136 Water bridges: C:Y.43, C:G.46, C:T.48, C:K.164 EDO.15: 9 residues within 4Å: Chain C: G.188, F.189, D.190, E.191, S.207, T.208, I.242, L.246, L.250 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.190, C:D.190 Water bridges: C:S.207, C:S.207 EDO.16: 3 residues within 4Å: Chain C: N.248, K.280, F.283 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.248, C:K.280 EDO.17: 3 residues within 4Å: Chain C: K.119, H.120, D.123 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.120, C:D.123 EDO.20: 7 residues within 4Å: Chain D: A.10, G.46, S.47, T.48, Y.136, I.138, K.164 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:T.48, D:T.48, D:Y.136, D:K.164 Water bridges: D:Y.43, D:G.46, D:T.48 EDO.21: 6 residues within 4Å: Chain D: F.189, D.190, E.191, T.208, L.246, L.250 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.190, D:D.190 Water bridges: D:S.207, D:S.207

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
C

D
D

N-acetylneuraminate lyase

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