SMTL ID : 2qga.1

Plasmodium vivax adenylosuccinate lyase Pv003765 with AMP bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 3 residues within 4Å: Chain A: N.281 Chain C: N.281 Ligands: CA.9 No protein-ligand interaction detected (PLIP) CA.5: 3 residues within 4Å: Chain B: N.281 Chain D: N.281 Ligands: CA.13 No protein-ligand interaction detected (PLIP) CA.9: 3 residues within 4Å: Chain A: N.281 Chain C: N.281 Ligands: CA.1 No protein-ligand interaction detected (PLIP) CA.13: 3 residues within 4Å: Chain B: N.281 Chain D: N.281 Ligands: CA.5 No protein-ligand interaction detected (PLIP)

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: R.395, V.434, Q.437 Chain B: V.218, K.221 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.437, A:Q.437 Water bridges: A:R.395, A:R.395 Salt bridges: A:R.395, B:K.221 SO4.3: 7 residues within 4Å: Chain A: T.169, H.170 Chain B: Q.247 Chain C: S.295, K.301, N.303 Ligands: AMP.8 10 PLIP interactions: 3 interactions with chain A, 6 interactions with chain C, 1 interactions with chain B Hydrogen bonds: A:T.169, A:T.169, C:S.295, C:N.303, B:Q.247 Salt bridges: A:H.170, C:K.301 Water bridges: C:S.295, C:S.296, C:T.297 SO4.6: 5 residues within 4Å: Chain A: V.218, K.221 Chain B: R.395, V.434, Q.437 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Salt bridges: A:K.221, B:R.395 Hydrogen bonds: B:Q.437, B:Q.437 Water bridges: B:R.395, B:R.395 SO4.7: 8 residues within 4Å: Chain A: Q.247 Chain B: T.169, H.170 Chain D: S.295, M.298, K.301, N.303 Ligands: AMP.4 9 PLIP interactions: 5 interactions with chain D, 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: D:S.295, D:N.303, A:Q.247, A:Q.247, B:T.169 Water bridges: D:S.296, D:T.297 Salt bridges: D:K.301, B:H.170 SO4.10: 5 residues within 4Å: Chain C: R.395, V.434, Q.437 Chain D: V.218, K.221 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Q.437, C:Q.437 Water bridges: C:R.395, C:R.395 Salt bridges: C:R.395, D:K.221 SO4.11: 7 residues within 4Å: Chain A: S.295, K.301, N.303 Chain C: T.169, H.170 Chain D: Q.247 Ligands: AMP.16 10 PLIP interactions: 1 interactions with chain D, 6 interactions with chain A, 3 interactions with chain C Hydrogen bonds: D:Q.247, A:S.295, A:N.303, C:T.169, C:T.169 Water bridges: A:S.295, A:S.296, A:T.297 Salt bridges: A:K.301, C:H.170 SO4.14: 5 residues within 4Å: Chain C: V.218, K.221 Chain D: R.395, V.434, Q.437 6 PLIP interactions: 1 interactions with chain C, 5 interactions with chain D Salt bridges: C:K.221, D:R.395 Hydrogen bonds: D:Q.437, D:Q.437 Water bridges: D:R.395, D:R.395 SO4.15: 8 residues within 4Å: Chain B: S.295, M.298, K.301, N.303 Chain C: Q.247 Chain D: T.169, H.170 Ligands: AMP.12 9 PLIP interactions: 5 interactions with chain B, 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: B:S.295, B:N.303, C:Q.247, C:Q.247, D:T.169 Water bridges: B:S.296, B:T.297 Salt bridges: B:K.301, D:H.170

4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.4: 17 residues within 4Å: Chain A: N.87, H.88, D.89, S.122, E.123, Q.247, R.335, L.337, S.340, T.341, R.344 Chain B: H.170 Chain D: R.14, Y.15, I.305, N.309 Ligands: SO4.7 19 PLIP interactions: 14 interactions with chain A, 5 interactions with chain D Hydrogen bonds: A:N.87, A:D.89, A:Q.247, A:Q.247, A:R.335, A:S.340, D:R.14, D:Y.15, D:Y.15, D:N.309 Water bridges: A:T.121, A:T.121, A:S.122, A:S.122, A:N.126, A:S.340 Salt bridges: A:R.344, D:R.14 pi-Stacking: A:H.88 AMP.8: 16 residues within 4Å: Chain A: H.170 Chain B: N.87, H.88, D.89, S.122, E.123, Q.247, R.335, L.337, S.340, T.341, R.344 Chain C: R.14, Y.15, N.309 Ligands: SO4.3 17 PLIP interactions: 12 interactions with chain B, 5 interactions with chain C Hydrogen bonds: B:N.87, B:D.89, B:D.89, B:Q.247, B:Q.247, B:R.335, B:S.340, C:R.14, C:Y.15, C:Y.15, C:N.309 Water bridges: B:T.121, B:N.126, B:T.341 Salt bridges: B:R.344, C:R.14 pi-Stacking: B:H.88 AMP.12: 17 residues within 4Å: Chain B: R.14, Y.15, I.305, N.309 Chain C: N.87, H.88, D.89, S.122, E.123, Q.247, R.335, L.337, S.340, T.341, R.344 Chain D: H.170 Ligands: SO4.15 18 PLIP interactions: 4 interactions with chain B, 14 interactions with chain C Hydrogen bonds: B:R.14, B:Y.15, B:N.309, C:N.87, C:D.89, C:E.123, C:Q.247, C:Q.247, C:R.335, C:S.340 Salt bridges: B:R.14, C:R.344 Water bridges: C:S.122, C:S.122, C:S.122, C:N.126, C:S.340 pi-Stacking: C:H.88 AMP.16: 16 residues within 4Å: Chain A: R.14, Y.15, N.309 Chain C: H.170 Chain D: N.87, H.88, D.89, S.122, E.123, Q.247, R.335, L.337, S.340, T.341, R.344 Ligands: SO4.11 16 PLIP interactions: 12 interactions with chain D, 4 interactions with chain A Hydrogen bonds: D:N.87, D:D.89, D:D.89, D:E.123, D:Q.247, D:Q.247, D:R.335, D:S.340, A:R.14, A:Y.15, A:N.309 Water bridges: D:N.126, D:T.341 Salt bridges: D:R.344, A:R.14 pi-Stacking: D:H.88

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lunin, V.V. et al., Plasmodium vivax adenylosuccinate lyase Pv003765 with AMP bound. To be Published

Release Date

2007-07-24

Peptides

Adenylosuccinate lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
B

D
C

Adenylosuccinate lyase