SMTL ID : 5nx9.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

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

CL.1: 5 residues within 4Å: Chain A: G.203, T.204, A.209, S.210 Chain B: Q.167 Ligand excluded by PLIP CL.2: 7 residues within 4Å: Chain A: A.113, T.114, Y.117, R.199, K.202, G.203, F.211 Ligand excluded by PLIP CL.10: 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.14: 4 residues within 4Å: Chain C: G.203, T.204, A.209, S.210 Ligand excluded by PLIP CL.15: 7 residues within 4Å: Chain C: A.113, T.114, Y.117, R.199, K.202, G.203, F.211 Ligand excluded by PLIP CL.21: 8 residues within 4Å: Chain D: A.113, T.114, Y.117, R.199, V.201, K.202, G.203, F.211 Ligand excluded by PLIP

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.3: 18 residues within 4Å: Chain A: E.84, R.88, H.89, D.90, S.115, Q.244, R.332, L.334, S.337, A.338, R.341 Chain B: H.162 Chain D: R.23, Y.24, G.291, M.302, R.306 Ligands: FUM.4 14 PLIP interactions: 10 interactions with chain A, 4 interactions with chain D Hydrogen bonds: A:E.84, A:R.88, A:D.90, A:Q.244, A:Q.244, A:R.332, A:S.337, D:Y.24 Water bridges: A:A.338, D:S.309 Salt bridges: A:R.341, D:R.23, D:R.306 pi-Stacking: A:H.89 AMP.22: 17 residues within 4Å: Chain A: R.23, Y.24, G.291, R.306 Chain C: H.162 Chain D: E.84, R.88, H.89, D.90, S.115, Q.244, R.332, L.334, S.337, A.338, R.341 Ligands: FUM.23 17 PLIP interactions: 6 interactions with chain A, 11 interactions with chain D Hydrogen bonds: A:Y.24, A:Y.24, D:E.84, D:R.88, D:D.90, D:Q.244, D:Q.244, D:R.332, D:S.337, D:S.337 Water bridges: A:N.300, A:S.309, D:A.338 Salt bridges: A:R.23, A:R.306, D:R.341 pi-Stacking: D:H.89

2 x FUM: FUMARIC ACID(Non-covalent)

FUM.4: 12 residues within 4Å: Chain A: H.89, T.114, S.115, Q.244 Chain B: T.161, H.162 Chain D: G.291, S.292, S.293, K.298, N.300 Ligands: AMP.3 10 PLIP interactions: 4 interactions with chain D, 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: D:G.291, D:S.293, D:N.300, B:T.161, A:S.115, A:S.115, A:Q.244 Salt bridges: D:K.298, B:H.162, A:H.89 FUM.23: 10 residues within 4Å: Chain A: G.291, K.298, N.300 Chain C: T.161, H.162 Chain D: H.89, T.114, S.115, Q.244 Ligands: AMP.22 11 PLIP interactions: 2 interactions with chain A, 7 interactions with chain D, 2 interactions with chain C Hydrogen bonds: 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 Water bridges: D:C.116

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

PEG.5: 4 residues within 4Å: Chain A: Q.419 Chain C: V.366, V.367, Y.368 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.419 PEG.6: 4 residues within 4Å: Chain A: H.220, E.223, Q.224, K.227 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.227 PEG.7: 5 residues within 4Å: Chain A: R.144, F.148, S.362, E.363, L.365 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.365 PEG.8: 7 residues within 4Å: Chain A: Q.187, E.466, E.467, P.470, L.471 Chain B: R.197, R.237 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.197, B:R.237, B:R.237 PEG.9: 5 residues within 4Å: Chain A: R.374, R.375, Q.378 Chain C: Q.378, V.417 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.378 PEG.12: 3 residues within 4Å: Chain B: T.55, M.228, K.232 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.232 Water bridges: B:K.232 PEG.16: 4 residues within 4Å: Chain C: H.220, E.223, Q.224, K.227 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.224, C:K.227 PEG.17: 2 residues within 4Å: Chain C: D.218, H.220 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.218 PEG.18: 2 residues within 4Å: Chain C: E.63, K.104 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.104 PEG.20: 4 residues within 4Å: Chain C: Q.213 Chain D: Q.167, N.387, S.451 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Q.213, D:Q.167, D:N.387 PEG.24: 1 residues within 4Å: Chain D: K.405 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.405 PEG.25: 4 residues within 4Å: Chain A: R.17 Chain D: F.77, K.78, A.81 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.17, A:R.17 PEG.26: 3 residues within 4Å: Chain A: N.360 Chain D: K.85, R.88 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Water bridges: D:R.88 Hydrogen bonds: A:N.360

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

2SA.11: 18 residues within 4Å: Chain A: T.161, H.162 Chain B: 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, N.300, M.302, R.306 19 PLIP interactions: 12 interactions with chain B, 5 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:D.90, B:T.114, B:S.115, B:S.115, B:Q.244, B:Q.244, B:Q.244, B:R.332, C:Y.24, C:Y.24, C:N.300, A:T.161 Water bridges: B:C.116 Salt bridges: B:H.89, B:R.341, C:R.23, C:R.306, A:H.162 pi-Stacking: B:H.89 2SA.13: 23 residues within 4Å: Chain B: R.23, Y.24, G.291, S.292, S.293, 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 30 PLIP interactions: 10 interactions with chain B, 18 interactions with chain C, 2 interactions with chain D Hydrogen bonds: B:S.293, B:N.300, C:E.84, C:E.84, C:D.90, C:T.114, C:T.114, C:S.115, C:S.115, C:Q.244, C:Q.244, C:Q.244, C:R.332, C:S.337, C:S.337, D:T.161 Water bridges: B:I.290, B:G.291, B:A.294, B:R.306, B:S.309, C:C.116, 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

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.19: 5 residues within 4Å: Chain C: L.56, G.57, L.214, F.215, E.216 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:L.56, C:F.215, C:E.216

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

Related Entries With Identical Sequence