SMTL ID : 6yb9.1

Human octameric PAICS in complex with SAICAR, AMP-PNP, and magnesium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

homo-octamer

Ligands

8 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 14 residues within 4Å: Chain A: Y.14, G.16, K.17, T.18, K.19, V.21, L.33, P.89, Q.90, C.91, M.93, K.131, D.207 Ligands: MG.7 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Y.14, A:G.16, A:K.17, A:T.18, A:T.18, A:K.19, A:P.89, A:C.91, A:K.131, A:K.131, A:D.207 Water bridges: A:E.193, A:D.207 Salt bridges: A:K.19 ANP.10: 14 residues within 4Å: Chain B: Y.14, G.16, K.17, T.18, K.19, V.21, L.33, P.89, Q.90, C.91, M.93, K.131, D.207 Ligands: MG.13 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:G.16, B:K.17, B:K.17, B:T.18, B:T.18, B:T.18, B:K.19, B:P.89, B:C.91, B:K.131, B:K.131, B:D.207 Water bridges: B:D.207 Salt bridges: B:K.19 ANP.15: 14 residues within 4Å: Chain C: Y.14, G.16, K.17, T.18, K.19, V.21, L.33, P.89, Q.90, C.91, M.93, K.131, D.207 Ligands: MG.21 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:Y.14, C:G.16, C:K.17, C:T.18, C:T.18, C:K.19, C:P.89, C:C.91, C:K.131, C:K.131, C:D.207 Water bridges: C:E.193, C:D.207 Salt bridges: C:K.19 ANP.24: 14 residues within 4Å: Chain D: Y.14, G.16, K.17, T.18, K.19, V.21, L.33, P.89, Q.90, C.91, M.93, K.131, D.207 Ligands: MG.27 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:G.16, D:K.17, D:K.17, D:T.18, D:T.18, D:T.18, D:K.19, D:P.89, D:C.91, D:K.131, D:K.131, D:D.207 Water bridges: D:D.207 Salt bridges: D:K.19 ANP.29: 14 residues within 4Å: Chain E: Y.14, G.16, K.17, T.18, K.19, V.21, L.33, P.89, Q.90, C.91, M.93, K.131, D.207 Ligands: MG.35 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:G.16, E:K.17, E:T.18, E:T.18, E:T.18, E:K.19, E:P.89, E:C.91, E:K.131, E:K.131, E:D.207 Water bridges: E:E.193, E:D.207 Salt bridges: E:K.19 ANP.38: 14 residues within 4Å: Chain F: Y.14, G.16, K.17, T.18, K.19, V.21, L.33, P.89, Q.90, C.91, M.93, K.131, D.207 Ligands: MG.41 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:G.16, F:K.17, F:K.17, F:T.18, F:T.18, F:K.19, F:P.89, F:C.91, F:K.131, F:K.131, F:D.207 Water bridges: F:D.207 Salt bridges: F:K.19 ANP.43: 14 residues within 4Å: Chain G: Y.14, G.16, K.17, T.18, K.19, V.21, L.33, P.89, Q.90, C.91, M.93, K.131, D.207 Ligands: MG.49 14 PLIP interactions: 14 interactions with chain G Hydrogen bonds: G:G.16, G:K.17, G:T.18, G:T.18, G:T.18, G:K.19, G:P.89, G:C.91, G:K.131, G:K.131, G:D.207 Water bridges: G:E.193, G:D.207 Salt bridges: G:K.19 ANP.52: 14 residues within 4Å: Chain H: Y.14, G.16, K.17, T.18, K.19, V.21, L.33, P.89, Q.90, C.91, M.93, K.131, D.207 Ligands: MG.55 14 PLIP interactions: 14 interactions with chain H Hydrogen bonds: H:G.16, H:K.17, H:K.17, H:K.17, H:T.18, H:T.18, H:K.19, H:P.89, H:C.91, H:K.131, H:K.131, H:D.207 Water bridges: H:D.207 Salt bridges: H:K.19

8 x OK8: (2~{S})-2-[[5-azanyl-1-[(2~{R},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]imidazol-4-yl]car bonylamino]butanedioic acid(Non-covalent)

OK8.2: 19 residues within 4Å: Chain A: K.17, T.40, A.41, G.42, E.97, V.99, R.101, G.106, S.107, D.189, M.190, K.191, D.212, S.213, W.214, R.215, K.228, R.232 Ligands: MG.8 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:G.42, A:S.107, A:S.107, A:D.189, A:D.212, A:W.214, A:R.232, A:R.232 Water bridges: A:T.40, A:S.107, A:K.228, A:K.228 Salt bridges: A:K.17, A:R.101, A:R.215, A:K.228, A:K.228, A:R.232 OK8.11: 20 residues within 4Å: Chain B: K.17, T.40, A.41, G.42, E.97, V.99, R.101, T.105, G.106, S.107, D.189, M.190, K.191, D.212, S.213, W.214, R.215, K.228, R.232 Ligands: MG.14 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:G.42, B:G.42, B:S.107, B:D.137, B:D.189, B:D.212, B:R.232, B:R.232 Water bridges: B:S.107, B:S.107, B:D.212, B:W.214, B:R.215, B:R.215 Salt bridges: B:K.17, B:R.101, B:R.215, B:K.228, B:K.228, B:R.232 OK8.16: 19 residues within 4Å: Chain C: K.17, T.40, A.41, G.42, E.97, V.99, R.101, G.106, S.107, D.189, M.190, K.191, D.212, S.213, W.214, R.215, K.228, R.232 Ligands: MG.22 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:G.42, C:S.107, C:S.107, C:D.189, C:D.212, C:W.214, C:R.232, C:R.232 Water bridges: C:T.40, C:S.107, C:K.228, C:K.228 Salt bridges: C:K.17, C:R.101, C:R.215, C:K.228, C:K.228, C:R.232 OK8.25: 20 residues within 4Å: Chain D: K.17, T.40, A.41, G.42, E.97, V.99, R.101, T.105, G.106, S.107, D.189, M.190, K.191, D.212, S.213, W.214, R.215, K.228, R.232 Ligands: MG.28 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: D:G.42, D:G.42, D:S.107, D:D.137, D:D.189, D:D.212, D:R.232, D:R.232 Water bridges: D:S.107, D:S.107, D:D.212, D:W.214, D:R.215, D:R.215 Salt bridges: D:K.17, D:R.101, D:R.215, D:K.228, D:K.228, D:R.232 OK8.30: 19 residues within 4Å: Chain E: K.17, T.40, A.41, G.42, E.97, V.99, R.101, G.106, S.107, D.189, M.190, K.191, D.212, S.213, W.214, R.215, K.228, R.232 Ligands: MG.36 18 PLIP interactions: 18 interactions with chain E Hydrogen bonds: E:T.40, E:G.42, E:S.107, E:S.107, E:D.189, E:D.212, E:W.214, E:R.232, E:R.232 Water bridges: E:S.107, E:K.228, E:K.228 Salt bridges: E:K.17, E:R.101, E:R.215, E:K.228, E:K.228, E:R.232 OK8.39: 20 residues within 4Å: Chain F: K.17, T.40, A.41, G.42, E.97, V.99, R.101, T.105, G.106, S.107, D.189, M.190, K.191, D.212, S.213, W.214, R.215, K.228, R.232 Ligands: MG.42 20 PLIP interactions: 20 interactions with chain F Hydrogen bonds: F:T.40, F:G.42, F:G.42, F:S.107, F:D.189, F:D.212, F:R.232, F:R.232 Water bridges: F:S.107, F:S.107, F:D.212, F:W.214, F:R.215, F:R.215 Salt bridges: F:K.17, F:R.101, F:R.215, F:K.228, F:K.228, F:R.232 OK8.44: 19 residues within 4Å: Chain G: K.17, T.40, A.41, G.42, E.97, V.99, R.101, G.106, S.107, D.189, M.190, K.191, D.212, S.213, W.214, R.215, K.228, R.232 Ligands: MG.50 18 PLIP interactions: 18 interactions with chain G Hydrogen bonds: G:T.40, G:G.42, G:S.107, G:S.107, G:D.189, G:D.212, G:W.214, G:R.232, G:R.232 Water bridges: G:S.107, G:K.228, G:K.228 Salt bridges: G:K.17, G:R.101, G:R.215, G:K.228, G:K.228, G:R.232 OK8.53: 20 residues within 4Å: Chain H: K.17, T.40, A.41, G.42, E.97, V.99, R.101, T.105, G.106, S.107, D.189, M.190, K.191, D.212, S.213, W.214, R.215, K.228, R.232 Ligands: MG.56 21 PLIP interactions: 21 interactions with chain H Hydrogen bonds: H:T.40, H:G.42, H:G.42, H:S.107, H:D.189, H:D.212, H:R.232, H:R.232 Water bridges: H:E.97, H:S.107, H:S.107, H:D.212, H:W.214, H:R.215, H:R.215 Salt bridges: H:K.17, H:R.101, H:R.215, H:K.228, H:K.228, H:R.232

24 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 7 residues within 4Å: Chain A: K.178, E.263, G.392, L.393, S.394, N.395, H.396 Ligand excluded by PLIP EDO.4: 7 residues within 4Å: Chain A: I.73, K.74, I.164, F.194, I.203, L.205, I.411 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: V.377, L.378, S.379 Chain B: L.366, R.367, L.368 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: E.317, G.318, D.319, G.320 Chain B: E.177, K.178 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain A: E.177, K.178, L.181 Chain B: E.317, G.318, D.319, G.320 Ligand excluded by PLIP EDO.12: 2 residues within 4Å: Chain B: S.274, T.275 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain C: K.178, E.263, G.392, L.393, S.394, N.395, H.396 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain C: I.73, K.74, I.164, F.194, I.203, L.205, I.411 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain C: V.377, L.378, S.379 Chain D: L.366, R.367, L.368 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain C: E.317, G.318, D.319, G.320 Chain D: E.177, K.178 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain C: E.177, K.178, L.181 Chain D: E.317, G.318, D.319, G.320 Ligand excluded by PLIP EDO.26: 2 residues within 4Å: Chain D: S.274, T.275 Ligand excluded by PLIP EDO.31: 7 residues within 4Å: Chain E: K.178, E.263, G.392, L.393, S.394, N.395, H.396 Ligand excluded by PLIP EDO.32: 7 residues within 4Å: Chain E: I.73, K.74, I.164, F.194, I.203, L.205, I.411 Ligand excluded by PLIP EDO.33: 6 residues within 4Å: Chain E: V.377, L.378, S.379 Chain F: L.366, R.367, L.368 Ligand excluded by PLIP EDO.34: 6 residues within 4Å: Chain E: E.317, G.318, D.319, G.320 Chain F: E.177, K.178 Ligand excluded by PLIP EDO.37: 7 residues within 4Å: Chain E: E.177, K.178, L.181 Chain F: E.317, G.318, D.319, G.320 Ligand excluded by PLIP EDO.40: 2 residues within 4Å: Chain F: S.274, T.275 Ligand excluded by PLIP EDO.45: 7 residues within 4Å: Chain G: K.178, E.263, G.392, L.393, S.394, N.395, H.396 Ligand excluded by PLIP EDO.46: 7 residues within 4Å: Chain G: I.73, K.74, I.164, F.194, I.203, L.205, I.411 Ligand excluded by PLIP EDO.47: 6 residues within 4Å: Chain G: V.377, L.378, S.379 Chain H: L.366, R.367, L.368 Ligand excluded by PLIP EDO.48: 6 residues within 4Å: Chain G: E.317, G.318, D.319, G.320 Chain H: E.177, K.178 Ligand excluded by PLIP EDO.51: 7 residues within 4Å: Chain G: E.177, K.178, L.181 Chain H: E.317, G.318, D.319, G.320 Ligand excluded by PLIP EDO.54: 2 residues within 4Å: Chain H: S.274, T.275 Ligand excluded by PLIP

16 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 2 residues within 4Å: Chain A: D.207 Ligands: ANP.1 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain A: E.97, D.137 Ligands: OK8.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.97, A:D.137 MG.13: 2 residues within 4Å: Chain B: D.207 Ligands: ANP.10 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain B: E.97, D.137 Ligands: OK8.11 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.97, B:D.137, H2O.11 MG.21: 2 residues within 4Å: Chain C: D.207 Ligands: ANP.15 No protein-ligand interaction detected (PLIP) MG.22: 3 residues within 4Å: Chain C: E.97, D.137 Ligands: OK8.16 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.97, C:D.137 MG.27: 2 residues within 4Å: Chain D: D.207 Ligands: ANP.24 No protein-ligand interaction detected (PLIP) MG.28: 3 residues within 4Å: Chain D: E.97, D.137 Ligands: OK8.25 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.97, D:D.137, H2O.22 MG.35: 2 residues within 4Å: Chain E: D.207 Ligands: ANP.29 No protein-ligand interaction detected (PLIP) MG.36: 3 residues within 4Å: Chain E: E.97, D.137 Ligands: OK8.30 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:E.97, E:D.137 MG.41: 2 residues within 4Å: Chain F: D.207 Ligands: ANP.38 No protein-ligand interaction detected (PLIP) MG.42: 3 residues within 4Å: Chain F: E.97, D.137 Ligands: OK8.39 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.97, F:D.137, H2O.33 MG.49: 2 residues within 4Å: Chain G: D.207 Ligands: ANP.43 No protein-ligand interaction detected (PLIP) MG.50: 3 residues within 4Å: Chain G: E.97, D.137 Ligands: OK8.44 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:E.97, G:D.137 MG.55: 2 residues within 4Å: Chain H: D.207 Ligands: ANP.52 No protein-ligand interaction detected (PLIP) MG.56: 3 residues within 4Å: Chain H: E.97, D.137 Ligands: OK8.53 3 PLIP interactions: 2 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:E.97, H:D.137, H2O.44

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Skerlova, J. et al., Crystal structures of human PAICS reveal substrate and product binding of an emerging cancer target. J.Biol.Chem. (2020)

Release Date

2020-07-08

Peptides

Multifunctional protein ADE2: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

Multifunctional protein ADE2

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