SMTL ID : 2ptq.1

Crystal structure of Escherichia coli adenylosuccinate lyase mutant H171N with bound AMP and fumarate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x FUM: FUMARIC ACID(Non-covalent)

FUM.1: 13 residues within 4Å: Chain A: S.295, S.296, T.297, M.298, K.301, N.303 Chain B: H.91, T.122, S.123, Q.247 Chain D: T.170, N.171 Ligands: AMP.4 9 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A, 2 interactions with chain D Hydrogen bonds: B:S.123, B:Q.247, A:S.296, A:N.303, D:T.170, D:N.171 Water bridges: B:E.124 Salt bridges: B:H.91, A:K.301 FUM.3: 13 residues within 4Å: Chain A: H.91, T.122, S.123, Q.247 Chain B: S.295, S.296, T.297, M.298, K.301, N.303 Chain C: T.170, N.171 Ligands: AMP.2 11 PLIP interactions: 3 interactions with chain B, 7 interactions with chain A, 1 interactions with chain C Hydrogen bonds: B:S.296, B:N.303, A:T.122, A:T.122, A:S.123, A:Q.247, A:Q.247, C:T.170 Salt bridges: B:K.301, A:H.91 Water bridges: A:E.124 FUM.5: 13 residues within 4Å: Chain B: T.170, N.171 Chain C: S.295, S.296, T.297, M.298, K.301, N.303 Chain D: H.91, T.122, S.123, Q.247 Ligands: AMP.8 9 PLIP interactions: 4 interactions with chain D, 2 interactions with chain B, 3 interactions with chain C Hydrogen bonds: D:S.123, D:Q.247, B:T.170, B:N.171, C:S.296, C:N.303 Water bridges: D:E.124 Salt bridges: D:H.91, C:K.301 FUM.7: 13 residues within 4Å: Chain A: T.170, N.171 Chain C: H.91, T.122, S.123, Q.247 Chain D: S.295, S.296, T.297, M.298, K.301, N.303 Ligands: AMP.6 11 PLIP interactions: 7 interactions with chain C, 3 interactions with chain D, 1 interactions with chain A Hydrogen bonds: C:T.122, C:T.122, C:S.123, C:Q.247, C:Q.247, D:S.296, D:N.303, A:T.170 Water bridges: C:E.124 Salt bridges: C:H.91, D:K.301

4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 19 residues within 4Å: Chain A: E.86, N.90, H.91, D.92, S.123, E.124, Q.247, R.335, L.337, S.340, T.341, R.344 Chain B: R.15, Y.16, N.303, I.305, N.309 Chain C: N.171 Ligands: FUM.3 19 PLIP interactions: 11 interactions with chain A, 7 interactions with chain B, 1 interactions with chain C Hydrogen bonds: A:E.86, A:N.90, A:D.92, A:Q.247, A:Q.247, A:R.335, A:S.340, B:R.15, B:Y.16, B:Y.16, B:Y.16, B:N.303, B:N.309, C:N.171 Water bridges: A:N.127, A:S.340, A:T.341 Salt bridges: A:R.344, B:R.15 AMP.4: 19 residues within 4Å: Chain A: R.15, Y.16, N.303, I.305, N.309 Chain B: E.86, N.90, H.91, D.92, S.123, E.124, Q.247, R.335, L.337, S.340, T.341, R.344 Chain D: N.171 Ligands: FUM.1 20 PLIP interactions: 13 interactions with chain B, 6 interactions with chain A, 1 interactions with chain D Hydrogen bonds: B:E.86, B:E.86, B:N.90, B:D.92, B:E.124, B:Q.247, B:Q.247, B:R.335, B:S.340, A:R.15, A:Y.16, A:Y.16, A:N.303, A:N.309, D:N.171 Water bridges: B:N.127, B:S.340, B:T.341 Salt bridges: B:R.344, A:R.15 AMP.6: 19 residues within 4Å: Chain A: N.171 Chain C: E.86, N.90, H.91, D.92, S.123, E.124, Q.247, R.335, L.337, S.340, T.341, R.344 Chain D: R.15, Y.16, N.303, I.305, N.309 Ligands: FUM.7 19 PLIP interactions: 7 interactions with chain D, 11 interactions with chain C, 1 interactions with chain A Hydrogen bonds: D:R.15, D:Y.16, D:Y.16, D:Y.16, D:N.303, D:N.309, C:E.86, C:N.90, C:D.92, C:Q.247, C:Q.247, C:R.335, C:S.340, A:N.171 Salt bridges: D:R.15, C:R.344 Water bridges: C:N.127, C:S.340, C:T.341 AMP.8: 19 residues within 4Å: Chain B: N.171 Chain C: R.15, Y.16, N.303, I.305, N.309 Chain D: E.86, N.90, H.91, D.92, S.123, E.124, Q.247, R.335, L.337, S.340, T.341, R.344 Ligands: FUM.5 20 PLIP interactions: 13 interactions with chain D, 6 interactions with chain C, 1 interactions with chain B Hydrogen bonds: D:E.86, D:E.86, D:N.90, D:D.92, D:E.124, D:Q.247, D:Q.247, D:R.335, D:S.340, C:R.15, C:Y.16, C:Y.16, C:N.303, C:N.309, B:N.171 Water bridges: D:N.127, D:S.340, D:T.341 Salt bridges: D:R.344, C:R.15

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsai, M. et al., Substrate and Product Complexes of Escherichia coli Adenylosuccinate Lyase Provide New Insights into the Enzymatic Mechanism. J.Mol.Biol. (2007)

Release Date

2007-07-03

Peptides

Adenylosuccinate lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Adenylosuccinate lyase