SMTL ID : 5nxa.2 (1 other biounit)

Crystal structure of Neanderthal Adenylosuccinate Lyase (ADSL)in complex with its products AICAR and fumarate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

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

CL.1: 6 residues within 4Å: Chain A: A.113, T.114, Y.117, R.199, K.202, G.203 Ligand excluded by PLIP CL.3: 7 residues within 4Å: Chain B: A.113, T.114, Y.117, R.199, K.202, G.203, F.211 Ligand excluded by PLIP CL.5: 5 residues within 4Å: Chain C: T.114, Y.117, R.199, K.202, G.203 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain D: T.114, Y.117, R.199, K.202, G.203 Ligand excluded by PLIP

1 x FUM: FUMARIC ACID(Non-covalent)

FUM.2: 13 residues within 4Å: Chain A: S.292, S.293, A.294, M.295, K.298, N.300 Chain C: T.161, H.162 Chain D: H.89, T.114, S.115, Q.244 Ligands: AMZ.9 12 PLIP interactions: 4 interactions with chain A, 6 interactions with chain D, 2 interactions with chain C Hydrogen bonds: A:S.293, A:A.294, A:N.300, D:T.114, D:S.115, D:S.115, D:Q.244, D:Q.244, C:T.161 Salt bridges: A:K.298, D:H.89, C:H.162

3 x SSS: N-{[5-AMINO-1-(5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-1H-IMIDAZOL-4-YL]CARBONYL}-L-ASPARTIC ACID(Non-covalent)

SSS.4: 20 residues within 4Å: Chain A: T.161, H.162 Chain B: E.84, R.88, H.89, D.90, T.114, S.115, Q.244, R.332, L.334, S.337, A.338, R.341 Chain C: R.23, Y.24, K.298, N.300, M.302, R.306 23 PLIP interactions: 13 interactions with chain B, 3 interactions with chain A, 7 interactions with chain C Hydrogen bonds: B:E.84, B:H.89, B:D.90, B:S.115, B:S.115, B:S.115, B:Q.244, B:S.337, B:S.337, A:T.161, A:H.162, C:R.23, C:Y.24, C:N.300 Water bridges: B:A.338, C:S.309 Salt bridges: B:H.89, B:R.341, A:H.162, C:R.23, C:K.298, C:R.306 pi-Stacking: B:H.89 SSS.6: 20 residues within 4Å: Chain B: R.23, Y.24, K.298, N.300, M.302, R.306 Chain C: E.84, R.88, H.89, D.90, T.114, S.115, Q.244, R.332, L.334, S.337, A.338, R.341 Chain D: T.161, H.162 24 PLIP interactions: 8 interactions with chain B, 13 interactions with chain C, 3 interactions with chain D Hydrogen bonds: B:R.23, B:Y.24, B:N.300, B:R.306, C:E.84, C:D.90, C:S.115, C:S.115, C:S.115, C:Q.244, C:R.332, C:S.337, C:S.337, D:T.161, D:H.162 Water bridges: B:S.309, C:A.338 Salt bridges: B:R.23, B:K.298, B:R.306, C:H.89, C:R.341, D:H.162 pi-Cation interactions: C:H.89 SSS.7: 25 residues within 4Å: Chain A: E.84, R.88, H.89, D.90, T.114, S.115, Q.244, R.332, L.334, S.337, A.338, R.341 Chain B: T.161, H.162 Chain D: R.23, Y.24, G.291, S.292, S.293, A.294, M.295, K.298, N.300, M.302, R.306 32 PLIP interactions: 19 interactions with chain A, 11 interactions with chain D, 2 interactions with chain B Hydrogen bonds: A:E.84, A:E.84, A:H.89, A:D.90, A:T.114, A:T.114, A:S.115, A:S.115, A:S.115, A:Q.244, A:Q.244, A:Q.244, A:R.332, A:S.337, A:S.337, D:R.23, D:Y.24, D:S.293, D:A.294, D:N.300, B:T.161 Water bridges: A:A.338, D:R.306, D:R.306, D:S.309 Salt bridges: A:H.89, A:R.341, D:R.23, D:K.298, D:R.306, B:H.162 pi-Cation interactions: A:H.89

1 x AMZ: AMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE(Non-covalent)

AMZ.9: 19 residues within 4Å: Chain A: R.23, Y.24, G.291, M.302, R.306 Chain C: H.162 Chain D: E.84, R.88, H.89, D.90, S.115, C.116, Q.244, R.332, L.334, S.337, A.338, R.341 Ligands: FUM.2 17 PLIP interactions: 13 interactions with chain D, 4 interactions with chain A Hydrogen bonds: D:E.84, D:R.88, D:D.90, D:S.115, D:S.115, D:Q.244, D:Q.244, D:R.332, D:S.337, D:S.337, D:S.337, A:R.23 Water bridges: D:A.338, A:S.309 Salt bridges: D:R.341, A:R.23, A:R.306

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Van Laer, B. et al., Molecular comparison of Neanderthal and Modern Human adenylosuccinate lyase. Sci Rep (2018)

Release Date

2018-05-30

Peptides

Adenylosuccinate lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

Adenylosuccinate lyase

Related Entries With Identical Sequence