SMTL ID : 2j91.1

Crystal structure of Human Adenylosuccinate Lyase in complex with AMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 15 residues within 4Å: Chain A: R.42, Y.43, M.321, R.325 Chain C: H.181 Chain D: R.107, H.108, D.109, S.134, Q.263, R.351, L.353, S.356, A.357, R.360 17 PLIP interactions: 11 interactions with chain D, 6 interactions with chain A Hydrogen bonds: D:R.107, D:D.109, D:Q.263, D:Q.263, D:R.351, D:S.356, D:A.357, A:R.42, A:Y.43, A:Y.43 Water bridges: D:S.134, D:S.356, A:N.319 Salt bridges: D:R.360, A:R.42, A:R.325 pi-Stacking: D:H.108 AMP.4: 15 residues within 4Å: Chain B: R.42, Y.43, M.321, R.325 Chain C: R.107, H.108, D.109, S.134, Q.263, R.351, L.353, S.356, A.357, R.360 Chain D: H.181 20 PLIP interactions: 7 interactions with chain B, 13 interactions with chain C Hydrogen bonds: B:R.42, B:Y.43, C:E.103, C:E.103, C:R.107, C:D.109, C:Q.263, C:Q.263, C:R.351, C:S.356, C:S.356 Water bridges: B:N.319, B:R.325, B:S.328, C:S.134, C:S.134, C:A.357 Salt bridges: B:R.42, B:R.325, C:R.360 AMP.7: 14 residues within 4Å: Chain A: H.181 Chain B: R.107, D.109, C.135, Q.263, R.351, L.353, S.356, A.357, R.360 Chain C: R.42, Y.43, M.321, R.325 17 PLIP interactions: 5 interactions with chain C, 12 interactions with chain B Hydrogen bonds: C:R.42, C:Y.43, C:Y.43, B:R.107, B:D.109, B:D.109, B:Q.263, B:Q.263, B:R.351, B:S.356 Salt bridges: C:R.42, C:R.325, B:R.360 Water bridges: B:R.351, B:R.351, B:S.356, B:A.357 AMP.10: 15 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 16 PLIP interactions: 11 interactions with chain A, 5 interactions with chain D Hydrogen bonds: A:R.107, A:D.109, A:Q.263, A:Q.263, A:R.351, A:S.356, A:S.356, D:R.42, D:Y.43 Water bridges: A:E.103, A:E.103, A:A.357, D:S.328 Salt bridges: A:R.360, D:R.42, D:R.325

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

CL.2: 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.5: 6 residues within 4Å: Chain B: T.133, Y.136, R.218, K.221, G.222, F.230 Ligand excluded by PLIP CL.8: 7 residues within 4Å: Chain C: A.132, T.133, Y.136, R.218, K.221, G.222, F.230 Ligand excluded by PLIP CL.11: 7 residues within 4Å: Chain D: A.132, T.133, Y.136, R.218, K.221, G.222, F.230 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 9 residues within 4Å: Chain A: K.57, W.61, D.109, G.138, D.139, 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.6: 6 residues within 4Å: Chain B: F.52, D.142, R.359, R.360, L.363, A.364 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.364 Water bridges: B:R.359 GOL.9: 9 residues within 4Å: Chain C: K.57, W.61, D.109, G.138, D.139, D.142, S.356, R.359, R.360 9 PLIP interactions: 9 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:D.142, C:S.356 GOL.12: 8 residues within 4Å: Chain B: Q.183, P.184, K.437 Chain D: K.298, E.301, Y.316, K.317, R.318 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:K.437, D:Y.316, D:R.318 Water bridges: D:R.318

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stenmark, P. et al., Crystal Structure of Human Adenylosuccinate Lyase. To be Published

Release Date

2006-11-07

Peptides

ADENYLOSUCCINATE LYASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

ADENYLOSUCCINATE LYASE