SMTL ID : 2vd6.1

Human adenylosuccinate lyase in complex with its substrate N6-(1,2- Dicarboxyethyl)-AMP, and its products AMP and fumarate.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 17 residues within 4Å: Chain A: R.107, H.108, D.109, S.134, Q.263, R.351, L.353, S.356, A.357, R.360 Chain B: H.181 Chain D: R.42, Y.43, M.321, R.325 Ligands: FUM.2, CL.4 16 PLIP interactions: 8 interactions with chain A, 7 interactions with chain D, 1 interactions with chain B Hydrogen bonds: A:E.103, A:R.107, A:D.109, A:Q.263, A:R.351, A:S.356, A:A.357, D:R.42, D:Y.43, D:Y.43, B:H.181 Salt bridges: A:R.360, D:R.42, D:R.325 Water bridges: D:R.325, D:R.325 AMP.11: 17 residues within 4Å: Chain B: R.42, Y.43, M.321, R.325 Chain C: E.103, R.107, H.108, D.109, S.134, Q.263, R.351, L.353, S.356, A.357, R.360 Chain D: H.181 Ligands: FUM.12 17 PLIP interactions: 10 interactions with chain C, 6 interactions with chain B, 1 interactions with chain D Hydrogen bonds: C:E.103, C:E.103, C:R.107, C:D.109, C:Q.263, C:R.351, C:S.356, B:R.42, B:Y.43, D:H.181 Water bridges: C:S.356, C:A.357, B:N.319, B:S.328 Salt bridges: C:R.360, B:R.42, B:R.325

2 x FUM: FUMARIC ACID(Non-covalent)

FUM.2: 10 residues within 4Å: Chain A: H.108, M.111, T.133, S.134, T.223, Q.263 Chain B: T.180, H.181 Chain D: K.317 Ligands: AMP.1 13 PLIP interactions: 4 interactions with chain D, 7 interactions with chain A, 2 interactions with chain B Water bridges: D:K.317, D:K.317, D:N.319, A:C.135 Salt bridges: D:K.317, A:H.108, B:H.181 Hydrophobic interactions: A:T.133 Hydrogen bonds: A:S.134, A:S.134, A:Q.263, A:Q.263, B:T.180 FUM.12: 9 residues within 4Å: Chain B: K.317, N.319 Chain C: H.108, T.133, S.134, Q.263 Chain D: T.180, H.181 Ligands: AMP.11 11 PLIP interactions: 2 interactions with chain B, 7 interactions with chain C, 2 interactions with chain D Hydrogen bonds: B:N.319, C:T.133, C:S.134, C:S.134, C:Q.263, C:Q.263, D:T.180 Salt bridges: B:K.317, C:H.108, D:H.181 Water bridges: C:C.135

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: K.57, W.61, D.109, G.138, D.142, S.356, R.359, R.360 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.57, A:D.109, A:D.142, A:R.359, A:R.360, A:R.360 Water bridges: A:S.356 GOL.7: 8 residues within 4Å: Chain B: K.57, W.61, D.109, G.138, D.142, S.356, R.359, R.360 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:K.57, B:D.109, B:G.138, B:R.359, B:R.360, B:R.360 Water bridges: B:D.109, B:D.139, B:D.142, B:S.356 GOL.8: 6 residues within 4Å: Chain B: F.52, D.142, R.359, R.360, L.363, A.364 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.142, B:D.142, B:R.360, B:L.363, B:A.364 Water bridges: B:R.359 GOL.13: 8 residues within 4Å: Chain C: K.57, W.61, D.109, G.138, D.142, S.356, R.359, R.360 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:K.57, C:D.109, C:D.142, C:S.356, C:R.359, C:R.360, C:R.360 Water bridges: C:S.356 GOL.16: 8 residues within 4Å: Chain D: K.57, W.61, D.109, G.138, D.142, S.356, R.359, R.360 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:K.57, D:D.109, D:G.138, D:S.356, D:R.359, D:R.360, D:R.360 Water bridges: D:D.109, D:D.139, D:S.356

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

CL.4: 4 residues within 4Å: Chain B: H.181 Chain D: N.319, M.321 Ligands: AMP.1 Ligand excluded by PLIP CL.5: 7 residues within 4Å: Chain A: A.132, T.133, Y.136, R.218, K.221, G.222, F.230 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: H.181 Chain C: N.319, M.321 Ligands: 2SA.6 Ligand excluded by PLIP CL.10: 7 residues within 4Å: Chain B: A.132, T.133, Y.136, R.218, K.221, G.222, F.230 Ligand excluded by PLIP CL.14: 8 residues within 4Å: Chain C: A.132, T.133, Y.136, R.218, V.220, K.221, G.222, F.230 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain A: N.319, M.321 Chain C: H.181 Ligands: 2SA.15 Ligand excluded by PLIP CL.18: 7 residues within 4Å: Chain D: A.132, T.133, Y.136, R.218, K.221, G.222, F.230 Ligand excluded by PLIP

2 x 2SA: 2-[9-(3,4-DIHYDROXY-5-PHOSPHONOOXYMETHYL-TETRAHYDRO-FURAN-2-YL)-9H-PURIN-6-YLAMINO]-SUCCINIC ACID(Non-covalent)

2SA.6: 20 residues within 4Å: Chain A: T.180, H.181 Chain B: R.107, H.108, D.109, T.133, S.134, Q.263, R.351, L.353, S.356, A.357, R.360 Chain C: R.42, Y.43, K.317, N.319, M.321, R.325 Ligands: CL.9 30 PLIP interactions: 12 interactions with chain C, 16 interactions with chain B, 2 interactions with chain A Hydrogen bonds: C:R.42, C:Y.43, C:Y.43, C:Y.43, C:N.319, B:D.109, B:T.133, B:S.134, B:S.134, B:Q.263, B:Q.263, B:Q.263, B:R.351, A:T.180 Water bridges: C:K.317, C:K.317, C:R.325, C:S.328, B:E.103, B:R.107, B:H.108, B:C.135, B:A.357 Salt bridges: C:R.42, C:K.317, C:R.325, B:H.108, B:R.360, A:H.181 pi-Stacking: B:H.108 2SA.15: 20 residues within 4Å: Chain A: R.42, Y.43, K.317, N.319, M.321, R.325 Chain C: T.180, H.181 Chain D: R.107, H.108, D.109, T.133, S.134, Q.263, R.351, L.353, S.356, A.357, R.360 Ligands: CL.17 29 PLIP interactions: 11 interactions with chain A, 16 interactions with chain D, 2 interactions with chain C Hydrogen bonds: A:R.42, A:Y.43, A:Y.43, A:Y.43, A:N.319, D:D.109, D:S.134, D:S.134, D:Q.263, D:Q.263, D:Q.263, D:R.351, D:S.356, D:A.357, C:T.180 Water bridges: A:K.317, A:K.317, A:S.328, D:E.103, D:R.107, D:H.108, D:C.135 Salt bridges: A:R.42, A:K.317, A:R.325, D:H.108, D:R.360, C:H.181 pi-Stacking: D:H.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stenmark, P. et al., Human Adenylosuccinate Lyase in Complex with its Substrate N6-(1,2-Dicarboxyethyl)-AMP, and its Products AMP and Fumarate. To be Published

Release Date

2007-10-23

Peptides

ADENYLOSUCCINATE LYASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

ADENYLOSUCCINATE LYASE