SMTL ID : 6yb8.1

Human octameric PAICS in complex with CAIR and SAICAR

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

homo-octamer

Ligands

12 x C2R: 5-AMINO-1-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL)-1H-IMIDAZOLE-4-CARBOXYLIC ACID(Non-covalent)

C2R.1: 17 residues within 4Å: Chain A: G.273, S.274, D.277, S.301, A.302, H.303, K.304, V.328, A.329, G.330, R.331, S.332, N.333, G.334, L.335 Chain E: P.369, S.370 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:G.273, A:S.274, A:D.277, A:D.277, A:A.302, A:H.303, A:G.330, A:G.330, A:S.332, A:G.334, A:L.335, E:S.370 Water bridges: A:K.304, A:K.304 Salt bridges: A:H.303, A:K.304 C2R.9: 17 residues within 4Å: Chain B: G.273, S.274, D.277, S.301, A.302, H.303, K.304, V.328, A.329, G.330, R.331, S.332, N.333, G.334, L.335 Chain D: P.369, S.370 14 PLIP interactions: 1 interactions with chain D, 13 interactions with chain B Hydrogen bonds: D:S.370, B:G.273, B:S.274, B:D.277, B:D.277, B:S.301, B:A.302, B:H.303, B:G.330, B:G.330, B:G.334, B:L.335 Salt bridges: B:H.303, B:K.304 C2R.10: 15 residues within 4Å: Chain B: 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, R.232 Ligands: IMD.11 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:S.107, B:S.107, B:D.212, B:W.214, B:R.232, B:R.232 Water bridges: B:K.110, B:K.191, B:D.212, B:R.215, B:D.227, B:R.232 Salt bridges: B:R.101, B:K.191, B:R.215 pi-Cation interactions: B:R.232 C2R.17: 17 residues within 4Å: Chain C: G.273, S.274, D.277, S.301, A.302, H.303, K.304, V.328, A.329, G.330, R.331, S.332, N.333, G.334, L.335 Chain G: P.369, S.370 16 PLIP interactions: 15 interactions with chain C, 1 interactions with chain G Hydrogen bonds: C:G.273, C:S.274, C:D.277, C:D.277, C:A.302, C:H.303, C:G.330, C:G.330, C:S.332, C:G.334, C:L.335, G:S.370 Water bridges: C:K.304, C:K.304 Salt bridges: C:H.303, C:K.304 C2R.25: 17 residues within 4Å: Chain B: P.369, S.370 Chain D: G.273, S.274, D.277, S.301, A.302, H.303, K.304, V.328, A.329, G.330, R.331, S.332, N.333, G.334, L.335 14 PLIP interactions: 13 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:G.273, D:S.274, D:D.277, D:D.277, D:S.301, D:A.302, D:H.303, D:G.330, D:G.330, D:G.334, D:L.335, B:S.370 Salt bridges: D:H.303, D:K.304 C2R.26: 15 residues within 4Å: Chain D: 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, R.232 Ligands: IMD.27 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:S.107, D:S.107, D:D.212, D:W.214, D:R.232, D:R.232 Water bridges: D:K.110, D:K.191, D:D.212, D:R.215, D:D.227, D:R.232 Salt bridges: D:R.101, D:K.191, D:R.215 pi-Cation interactions: D:R.232 C2R.33: 17 residues within 4Å: Chain A: P.369, S.370 Chain E: G.273, S.274, D.277, S.301, A.302, H.303, K.304, V.328, A.329, G.330, R.331, S.332, N.333, G.334, L.335 16 PLIP interactions: 15 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:G.273, E:S.274, E:D.277, E:D.277, E:A.302, E:H.303, E:G.330, E:G.330, E:S.332, E:G.334, E:L.335, A:S.370 Water bridges: E:K.304, E:K.304 Salt bridges: E:H.303, E:K.304 C2R.41: 17 residues within 4Å: Chain F: G.273, S.274, D.277, S.301, A.302, H.303, K.304, V.328, A.329, G.330, R.331, S.332, N.333, G.334, L.335 Chain H: P.369, S.370 14 PLIP interactions: 13 interactions with chain F, 1 interactions with chain H Hydrogen bonds: F:G.273, F:S.274, F:D.277, F:D.277, F:S.301, F:A.302, F:H.303, F:G.330, F:G.330, F:G.334, F:L.335, H:S.370 Salt bridges: F:H.303, F:K.304 C2R.42: 15 residues within 4Å: Chain F: 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, R.232 Ligands: IMD.43 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:S.107, F:S.107, F:D.212, F:W.214, F:R.232, F:R.232 Water bridges: F:K.110, F:K.191, F:D.212, F:R.215, F:D.227, F:R.232 Salt bridges: F:R.101, F:K.191, F:R.215 pi-Cation interactions: F:R.232 C2R.49: 17 residues within 4Å: Chain C: P.369, S.370 Chain G: G.273, S.274, D.277, S.301, A.302, H.303, K.304, V.328, A.329, G.330, R.331, S.332, N.333, G.334, L.335 16 PLIP interactions: 1 interactions with chain C, 15 interactions with chain G Hydrogen bonds: C:S.370, G:G.273, G:S.274, G:D.277, G:D.277, G:A.302, G:H.303, G:G.330, G:G.330, G:S.332, G:G.334, G:L.335 Water bridges: G:K.304, G:K.304 Salt bridges: G:H.303, G:K.304 C2R.57: 17 residues within 4Å: Chain F: P.369, S.370 Chain H: G.273, S.274, D.277, S.301, A.302, H.303, K.304, V.328, A.329, G.330, R.331, S.332, N.333, G.334, L.335 14 PLIP interactions: 13 interactions with chain H, 1 interactions with chain F Hydrogen bonds: H:G.273, H:S.274, H:D.277, H:D.277, H:S.301, H:A.302, H:H.303, H:G.330, H:G.330, H:G.334, H:L.335, F:S.370 Salt bridges: H:H.303, H:K.304 C2R.58: 15 residues within 4Å: Chain H: 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, R.232 Ligands: IMD.59 16 PLIP interactions: 16 interactions with chain H Hydrogen bonds: H:S.107, H:S.107, H:D.212, H:W.214, H:R.232, H:R.232 Water bridges: H:K.110, H:K.191, H:D.212, H:R.215, H:D.227, H:R.232 Salt bridges: H:R.101, H:K.191, H:R.215 pi-Cation interactions: H:R.232

4 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: 20 residues within 4Å: Chain A: K.17, A.41, G.42, N.43, E.97, V.99, R.101, G.106, S.107, D.137, D.189, M.190, K.191, D.212, S.213, W.214, R.215, K.228, R.232 Ligands: IMD.3 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:G.42, A:N.43, A:S.107, A:D.189, A:W.214, A:R.232, A:R.232 Water bridges: A:K.17, A:S.107, A:S.107, A:D.212, A:R.215, A:R.215, A:K.228 Salt bridges: A:K.17, A:R.101, A:R.215, A:K.228, A:R.232 pi-Cation interactions: A:R.232 OK8.18: 20 residues within 4Å: Chain C: K.17, A.41, G.42, N.43, E.97, V.99, R.101, G.106, S.107, D.137, D.189, M.190, K.191, D.212, S.213, W.214, R.215, K.228, R.232 Ligands: IMD.19 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:G.42, C:N.43, C:S.107, C:D.189, C:W.214, C:R.232, C:R.232 Water bridges: C:K.17, C:S.107, C:S.107, C:D.212, C:R.215, C:R.215, C:K.228 Salt bridges: C:K.17, C:R.101, C:R.215, C:K.228, C:R.232 pi-Cation interactions: C:R.232 OK8.34: 20 residues within 4Å: Chain E: K.17, A.41, G.42, N.43, E.97, V.99, R.101, G.106, S.107, D.137, D.189, M.190, K.191, D.212, S.213, W.214, R.215, K.228, R.232 Ligands: IMD.35 20 PLIP interactions: 20 interactions with chain E Hydrogen bonds: E:G.42, E:N.43, E:S.107, E:D.189, E:W.214, E:R.232, E:R.232 Water bridges: E:K.17, E:S.107, E:S.107, E:D.212, E:R.215, E:R.215, E:K.228 Salt bridges: E:K.17, E:R.101, E:R.215, E:K.228, E:R.232 pi-Cation interactions: E:R.232 OK8.50: 20 residues within 4Å: Chain G: K.17, A.41, G.42, N.43, E.97, V.99, R.101, G.106, S.107, D.137, D.189, M.190, K.191, D.212, S.213, W.214, R.215, K.228, R.232 Ligands: IMD.51 20 PLIP interactions: 20 interactions with chain G Hydrogen bonds: G:G.42, G:N.43, G:S.107, G:D.189, G:W.214, G:R.232, G:R.232 Water bridges: G:K.17, G:S.107, G:S.107, G:D.212, G:R.215, G:R.215, G:K.228 Salt bridges: G:K.17, G:R.101, G:R.215, G:K.228, G:R.232 pi-Cation interactions: G:R.232

8 x IMD: IMIDAZOLE(Non-covalent)

IMD.3: 4 residues within 4Å: Chain A: E.97, V.99, F.129 Ligands: OK8.2 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.107 IMD.11: 5 residues within 4Å: Chain B: E.97, V.99, F.129, D.137 Ligands: C2R.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.107, B:S.107 IMD.19: 4 residues within 4Å: Chain C: E.97, V.99, F.129 Ligands: OK8.18 1 PLIP interactions: 1 interactions with chain C Water bridges: C:S.107 IMD.27: 5 residues within 4Å: Chain D: E.97, V.99, F.129, D.137 Ligands: C2R.26 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.107, D:S.107 IMD.35: 4 residues within 4Å: Chain E: E.97, V.99, F.129 Ligands: OK8.34 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:E.97 Water bridges: E:S.107 IMD.43: 5 residues within 4Å: Chain F: E.97, V.99, F.129, D.137 Ligands: C2R.42 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:E.97, F:S.107, F:S.107 IMD.51: 4 residues within 4Å: Chain G: E.97, V.99, F.129 Ligands: OK8.50 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:E.97 Water bridges: G:S.107 IMD.59: 5 residues within 4Å: Chain H: E.97, V.99, F.129, D.137 Ligands: C2R.58 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:E.97, H:S.107, H:S.107

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

EDO.4: 8 residues within 4Å: Chain A: I.73, K.74, A.168, F.194, I.203, V.204, L.205, I.411 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain A: E.315, D.319 Chain B: Y.122 Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain A: V.31, L.33, P.89, Q.90, C.91, A.206, D.207 Ligand excluded by PLIP EDO.7: 8 residues within 4Å: Chain A: E.317, G.318, D.319, G.320, Y.345 Chain B: E.177, K.178, L.181 Ligand excluded by PLIP EDO.8: 8 residues within 4Å: Chain A: R.102, E.177, K.178, L.181 Chain B: E.317, G.318, D.319, G.320 Ligand excluded by PLIP EDO.12: 8 residues within 4Å: Chain B: I.73, K.74, A.168, F.194, I.203, V.204, L.205, I.411 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: Y.122 Chain B: E.315, Y.316, D.319 Ligand excluded by PLIP EDO.14: 9 residues within 4Å: Chain B: V.31, L.33, A.76, P.89, Q.90, C.91, M.93, A.206, D.207 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain B: S.262, G.292, P.294, N.395, V.398 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain B: G.118, Y.119, K.120 Ligand excluded by PLIP EDO.20: 8 residues within 4Å: Chain C: I.73, K.74, A.168, F.194, I.203, V.204, L.205, I.411 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain C: E.315, D.319 Chain D: Y.122 Ligand excluded by PLIP EDO.22: 7 residues within 4Å: Chain C: V.31, L.33, P.89, Q.90, C.91, A.206, D.207 Ligand excluded by PLIP EDO.23: 8 residues within 4Å: Chain C: E.317, G.318, D.319, G.320, Y.345 Chain D: E.177, K.178, L.181 Ligand excluded by PLIP EDO.24: 8 residues within 4Å: Chain C: R.102, E.177, K.178, L.181 Chain D: E.317, G.318, D.319, G.320 Ligand excluded by PLIP EDO.28: 8 residues within 4Å: Chain D: I.73, K.74, A.168, F.194, I.203, V.204, L.205, I.411 Ligand excluded by PLIP EDO.29: 4 residues within 4Å: Chain C: Y.122 Chain D: E.315, Y.316, D.319 Ligand excluded by PLIP EDO.30: 9 residues within 4Å: Chain D: V.31, L.33, A.76, P.89, Q.90, C.91, M.93, A.206, D.207 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain D: S.262, G.292, P.294, N.395, V.398 Ligand excluded by PLIP EDO.32: 3 residues within 4Å: Chain D: G.118, Y.119, K.120 Ligand excluded by PLIP EDO.36: 8 residues within 4Å: Chain E: I.73, K.74, A.168, F.194, I.203, V.204, L.205, I.411 Ligand excluded by PLIP EDO.37: 3 residues within 4Å: Chain E: E.315, D.319 Chain F: Y.122 Ligand excluded by PLIP EDO.38: 7 residues within 4Å: Chain E: V.31, L.33, P.89, Q.90, C.91, A.206, D.207 Ligand excluded by PLIP EDO.39: 8 residues within 4Å: Chain E: E.317, G.318, D.319, G.320, Y.345 Chain F: E.177, K.178, L.181 Ligand excluded by PLIP EDO.40: 8 residues within 4Å: Chain E: R.102, E.177, K.178, L.181 Chain F: E.317, G.318, D.319, G.320 Ligand excluded by PLIP EDO.44: 8 residues within 4Å: Chain F: I.73, K.74, A.168, F.194, I.203, V.204, L.205, I.411 Ligand excluded by PLIP EDO.45: 4 residues within 4Å: Chain E: Y.122 Chain F: E.315, Y.316, D.319 Ligand excluded by PLIP EDO.46: 9 residues within 4Å: Chain F: V.31, L.33, A.76, P.89, Q.90, C.91, M.93, A.206, D.207 Ligand excluded by PLIP EDO.47: 5 residues within 4Å: Chain F: S.262, G.292, P.294, N.395, V.398 Ligand excluded by PLIP EDO.48: 3 residues within 4Å: Chain F: G.118, Y.119, K.120 Ligand excluded by PLIP EDO.52: 8 residues within 4Å: Chain G: I.73, K.74, A.168, F.194, I.203, V.204, L.205, I.411 Ligand excluded by PLIP EDO.53: 3 residues within 4Å: Chain G: E.315, D.319 Chain H: Y.122 Ligand excluded by PLIP EDO.54: 7 residues within 4Å: Chain G: V.31, L.33, P.89, Q.90, C.91, A.206, D.207 Ligand excluded by PLIP EDO.55: 8 residues within 4Å: Chain G: E.317, G.318, D.319, G.320, Y.345 Chain H: E.177, K.178, L.181 Ligand excluded by PLIP EDO.56: 8 residues within 4Å: Chain G: R.102, E.177, K.178, L.181 Chain H: E.317, G.318, D.319, G.320 Ligand excluded by PLIP EDO.60: 8 residues within 4Å: Chain H: I.73, K.74, A.168, F.194, I.203, V.204, L.205, I.411 Ligand excluded by PLIP EDO.61: 4 residues within 4Å: Chain G: Y.122 Chain H: E.315, Y.316, D.319 Ligand excluded by PLIP EDO.62: 9 residues within 4Å: Chain H: V.31, L.33, A.76, P.89, Q.90, C.91, M.93, A.206, D.207 Ligand excluded by PLIP EDO.63: 5 residues within 4Å: Chain H: S.262, G.292, P.294, N.395, V.398 Ligand excluded by PLIP EDO.64: 3 residues within 4Å: Chain H: G.118, Y.119, K.120 Ligand excluded by PLIP

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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