SMTL ID : 5nx8.1

Crystal structure of Neanderthal Adenylosuccinate Lyase (ADSL)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

5 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 4 residues within 4Å: Chain A: L.58, P.59, L.111, L.214 No protein-ligand interaction detected (PLIP) PEG.2: 8 residues within 4Å: Chain A: L.124, D.195, L.196, R.197, F.239, V.250, E.253 Chain B: M.184 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.197 PEG.10: 3 residues within 4Å: Chain C: H.220, K.221, Q.224 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.218, C:H.220 PEG.11: 9 residues within 4Å: Chain C: L.124, D.195, L.196, R.197, F.239, Y.246, V.250, E.253 Chain D: M.184 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.197, C:E.253 Water bridges: C:R.197 PEG.16: 1 residues within 4Å: Chain D: P.470 No protein-ligand interaction detected (PLIP)

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: F.33, D.123, R.340, R.341, L.344, A.345 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.340, A:A.345 Water bridges: A:R.340 GOL.4: 5 residues within 4Å: Chain A: L.212, D.219 Chain B: G.454, R.455, Q.458 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Water bridges: A:G.217, A:D.219 Hydrogen bonds: B:G.454, B:Q.458 GOL.7: 6 residues within 4Å: Chain B: F.33, D.123, R.340, R.341, L.344, A.345 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.340, B:A.345 Water bridges: B:R.340 GOL.12: 6 residues within 4Å: Chain C: F.33, D.123, R.340, R.341, L.344, A.345 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:A.345 Water bridges: C:F.33, C:S.337, C:R.340, C:R.341 GOL.13: 5 residues within 4Å: Chain C: L.212, D.219 Chain D: G.454, R.455, Q.458 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:G.454, D:Q.458 Water bridges: C:G.217, C:D.219 GOL.17: 7 residues within 4Å: Chain D: F.33, D.123, I.126, R.340, R.341, L.344, A.345 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.123, D:A.345 Water bridges: D:F.33, D:R.340 GOL.18: 5 residues within 4Å: Chain C: G.454, R.455, Q.458 Chain D: L.212, D.219 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:D.219, C:G.454 Water bridges: C:S.450, C:G.454

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

CL.5: 4 residues within 4Å: Chain A: G.203, T.204, A.209, S.210 Ligand excluded by PLIP CL.6: 6 residues within 4Å: Chain A: T.114, Y.117, R.199, K.202, G.203, F.211 Ligand excluded by PLIP CL.8: 6 residues within 4Å: Chain B: T.114, Y.117, R.199, K.202, G.203, F.211 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain B: G.203, T.204, A.209, S.210 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain C: G.203, T.204, A.209, S.210 Ligand excluded by PLIP CL.15: 6 residues within 4Å: Chain C: T.114, Y.117, R.199, K.202, G.203, F.211 Ligand excluded by PLIP CL.19: 6 residues within 4Å: Chain D: T.114, Y.117, R.199, K.202, G.203, F.211 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain C: Q.167 Chain D: G.203, T.204, A.209, S.210 Ligand excluded by PLIP CL.21: 1 residues within 4Å: Chain D: A.139 Ligand excluded by PLIP

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
A

B
B

C
C

D
D

Adenylosuccinate lyase

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