SMTL ID : 4efc.1 (4 other biounits)

Crystal Structure of Adenylosuccinate Lyase from Trypanosoma Brucei, Tb427tmp.160.5560

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 20 residues within 4Å: Chain A: N.107, H.108, D.109, S.139, Q.140, N.143, Q.263, R.351, L.353, S.356, T.357, R.360 Chain B: R.30, Y.31, G.310, N.319, I.321, N.325 Chain C: H.186 Ligands: EDO.6 18 PLIP interactions: 6 interactions with chain B, 12 interactions with chain A Hydrogen bonds: B:R.30, B:Y.31, B:Y.31, B:N.319, B:N.325, A:E.103, A:N.107, A:D.109, A:Q.263, A:R.351, A:S.356 Salt bridges: B:R.30, A:R.360 Water bridges: A:S.139, A:S.139, A:N.143, A:S.356 pi-Stacking: A:H.108 AMP.5: 20 residues within 4Å: Chain A: R.30, Y.31, G.310, N.319, I.321, N.325 Chain B: N.107, H.108, D.109, S.139, Q.140, N.143, Q.263, R.351, L.353, S.356, T.357, R.360 Chain D: H.186 Ligands: EDO.3 19 PLIP interactions: 14 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:N.107, B:D.109, B:Q.263, B:R.351, B:S.356, A:R.30, A:Y.31, A:N.319, A:N.325 Water bridges: B:E.103, B:N.107, B:S.139, B:S.139, B:Q.140, B:N.143, B:T.357 Salt bridges: B:R.360, A:R.30 pi-Stacking: B:H.108 AMP.9: 20 residues within 4Å: Chain A: H.186 Chain C: N.107, H.108, D.109, S.139, Q.140, N.143, Q.263, R.351, L.353, S.356, T.357, R.360 Chain D: R.30, Y.31, G.310, N.319, I.321, N.325 Ligands: EDO.14 18 PLIP interactions: 12 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:E.103, C:N.107, C:D.109, C:Q.263, C:R.351, C:S.356, D:R.30, D:Y.31, D:Y.31, D:N.319, D:N.325 Water bridges: C:S.139, C:S.139, C:N.143, C:S.356 Salt bridges: C:R.360, D:R.30 pi-Stacking: C:H.108 AMP.13: 20 residues within 4Å: Chain B: H.186 Chain C: R.30, Y.31, G.310, N.319, I.321, N.325 Chain D: N.107, H.108, D.109, S.139, Q.140, N.143, Q.263, R.351, L.353, S.356, T.357, R.360 Ligands: EDO.11 19 PLIP interactions: 5 interactions with chain C, 14 interactions with chain D Hydrogen bonds: C:R.30, C:Y.31, C:N.319, C:N.325, D:N.107, D:D.109, D:Q.263, D:R.351, D:S.356 Salt bridges: C:R.30, D:R.360 Water bridges: D:E.103, D:N.107, D:S.139, D:S.139, D:Q.140, D:N.143, D:T.357 pi-Stacking: D:H.108

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.286, D.290 Chain C: S.347, R.348, L.349 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: C:S.347, C:L.349, A:D.290, H2O.4 MG.4: 1 residues within 4Å: Chain A: R.73 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:R.73, H2O.14, H2O.15, H2O.15 MG.7: 5 residues within 4Å: Chain B: S.347, R.348, L.349 Chain D: D.286, D.290 5 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: D:D.286, D:D.290, B:S.347, B:L.349, H2O.26 MG.10: 5 residues within 4Å: Chain A: S.347, R.348, L.349 Chain C: D.286, D.290 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: A:S.347, A:L.349, C:D.290, H2O.31 MG.12: 1 residues within 4Å: Chain C: R.73 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:R.73, H2O.41, H2O.42, H2O.42 MG.15: 5 residues within 4Å: Chain B: D.286, D.290 Chain D: S.347, R.348, L.349 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: B:D.286, B:D.290, D:S.347, D:L.349, H2O.54

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

EDO.3: 8 residues within 4Å: Chain A: S.311, M.314, K.317, N.319 Chain B: Q.263 Chain D: T.185, H.186 Ligands: AMP.5 4 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: D:T.185, D:H.186, A:N.319, B:Q.263 EDO.6: 9 residues within 4Å: Chain A: Q.263 Chain B: S.311, M.314, K.317, N.319 Chain C: T.185, H.186, A.190 Ligands: AMP.1 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: C:T.185, C:H.186, A:Q.263, B:K.317, B:N.319 EDO.11: 8 residues within 4Å: Chain B: T.185, H.186 Chain C: S.311, M.314, K.317, N.319 Chain D: Q.263 Ligands: AMP.13 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: B:T.185, B:H.186, C:N.319, D:Q.263 EDO.14: 9 residues within 4Å: Chain A: T.185, H.186, A.190 Chain C: Q.263 Chain D: S.311, M.314, K.317, N.319 Ligands: AMP.9 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D, 2 interactions with chain A Hydrogen bonds: C:Q.263, D:K.317, D:N.319, A:T.185, A:H.186

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

NA.8: 4 residues within 4Å: Chain B: D.275, N.338 Chain D: D.275 Ligands: NA.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.275, B:N.338 NA.16: 4 residues within 4Å: Chain B: D.275 Chain D: D.275, N.338 Ligands: NA.8 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:D.275 Water bridges: D:D.275, D:D.275, D:D.275, D:D.275, B:D.275

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wernimont, A.K. et al., Crystal Structure of Adenylosuccinate Lyase from Trypanosoma Brucei, Tb427tmp.160.5560. To be Published

Release Date

2013-02-13

Peptides

Adenylosuccinate lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Adenylosuccinate lyase

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