- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.25 Å
- Oligo State
- homo-octamer
- Ligands
- 8 x 5GP: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)
- 24 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)
GDP.2: 16 residues within 4Å:- Chain A: I.166, I.167, T.168, S.169, R.170, D.171, T.187, D.189, V.190, I.191, K.211, G.212, K.213
- Chain B: R.170, K.210
- Ligands: GDP.3
17 PLIP interactions:14 interactions with chain A, 3 interactions with chain B- Hydrogen bonds: A:T.168, A:S.169, A:S.169, A:D.171, A:T.187, A:T.187, A:I.191, A:K.211, A:G.212
- Water bridges: A:S.169, A:K.213, A:K.213, A:K.213, B:K.211
- Salt bridges: A:D.189, B:R.170, B:R.170
GDP.3: 17 residues within 4Å:- Chain A: K.118, Y.119, E.120, N.121, I.124, P.127, V.128, F.148, A.149, G.150, K.213, M.226, S.228, T.230, D.231, K.234
- Ligands: GDP.2
20 PLIP interactions:20 interactions with chain A- Hydrogen bonds: A:Y.119, A:N.121, A:N.121, A:V.128, A:A.149, A:G.150, A:G.150, A:K.213, A:S.228, A:T.230, A:D.231, A:K.234
- Water bridges: A:K.118, A:G.150, A:S.169, A:T.230
- Salt bridges: A:K.213, A:K.213
- pi-Stacking: A:F.148
- pi-Cation interactions: A:F.148
GDP.4: 14 residues within 4Å:- Chain A: E.120, N.121, G.122, L.199, E.200, N.203, K.207, L.227, S.228, D.231, L.232, N.235, K.243, K.248
10 PLIP interactions:10 interactions with chain A- Hydrogen bonds: A:E.120, A:N.121, A:E.200, A:N.203, A:N.203, A:K.243, A:K.248
- Water bridges: A:N.235
- Salt bridges: A:K.243, A:K.248
GDP.8: 16 residues within 4Å:- Chain A: R.170, K.210
- Chain B: I.166, I.167, T.168, S.169, R.170, D.171, T.187, D.189, V.190, I.191, K.211, G.212, K.213
- Ligands: GDP.9
22 PLIP interactions:19 interactions with chain B, 3 interactions with chain A- Hydrogen bonds: B:T.168, B:S.169, B:S.169, B:S.169, B:R.170, B:R.170, B:D.171, B:T.187, B:T.187, B:I.191, B:K.211, B:G.212, A:K.210
- Water bridges: B:D.189, B:D.189, B:K.213, B:K.213
- Salt bridges: B:R.170, B:K.211, A:R.170, A:R.170
- pi-Cation interactions: B:K.211
GDP.9: 17 residues within 4Å:- Chain B: K.118, Y.119, E.120, N.121, I.124, P.127, V.128, F.148, A.149, G.150, K.213, M.226, S.228, T.230, D.231, K.234
- Ligands: GDP.8
20 PLIP interactions:20 interactions with chain B- Hydrogen bonds: B:Y.119, B:N.121, B:N.121, B:V.128, B:A.149, B:G.150, B:G.150, B:K.213, B:S.228, B:T.230, B:D.231, B:K.234
- Water bridges: B:K.118, B:A.149, B:G.150, B:S.169
- Salt bridges: B:K.213, B:K.213
- pi-Stacking: B:F.148
- pi-Cation interactions: B:F.148
GDP.10: 14 residues within 4Å:- Chain B: E.120, N.121, G.122, L.199, E.200, N.203, L.227, S.228, D.231, L.232, N.235, P.239, K.243, K.248
10 PLIP interactions:10 interactions with chain B- Hydrogen bonds: B:N.121, B:N.203, B:N.203, B:N.235, B:N.235, B:K.243
- Water bridges: B:N.235, B:N.235, B:P.239
- Salt bridges: B:K.243
GDP.14: 16 residues within 4Å:- Chain C: I.166, I.167, T.168, S.169, R.170, D.171, T.187, D.189, V.190, I.191, K.211, G.212, K.213
- Chain D: R.170, K.210
- Ligands: GDP.15
17 PLIP interactions:14 interactions with chain C, 3 interactions with chain D- Hydrogen bonds: C:T.168, C:S.169, C:S.169, C:D.171, C:T.187, C:T.187, C:I.191, C:K.211, C:G.212
- Water bridges: C:S.169, C:K.213, C:K.213, C:K.213, D:K.211
- Salt bridges: C:D.189, D:R.170, D:R.170
GDP.15: 17 residues within 4Å:- Chain C: K.118, Y.119, E.120, N.121, I.124, P.127, V.128, F.148, A.149, G.150, K.213, M.226, S.228, T.230, D.231, K.234
- Ligands: GDP.14
20 PLIP interactions:20 interactions with chain C- Hydrogen bonds: C:Y.119, C:N.121, C:N.121, C:V.128, C:A.149, C:G.150, C:G.150, C:K.213, C:S.228, C:T.230, C:D.231, C:K.234
- Water bridges: C:K.118, C:G.150, C:S.169, C:T.230
- Salt bridges: C:K.213, C:K.213
- pi-Stacking: C:F.148
- pi-Cation interactions: C:F.148
GDP.16: 14 residues within 4Å:- Chain C: E.120, N.121, G.122, L.199, E.200, N.203, K.207, L.227, S.228, D.231, L.232, N.235, K.243, K.248
10 PLIP interactions:10 interactions with chain C- Hydrogen bonds: C:E.120, C:N.121, C:E.200, C:N.203, C:N.203, C:K.243, C:K.248
- Water bridges: C:N.235
- Salt bridges: C:K.243, C:K.248
GDP.20: 16 residues within 4Å:- Chain C: R.170, K.210
- Chain D: I.166, I.167, T.168, S.169, R.170, D.171, T.187, D.189, V.190, I.191, K.211, G.212, K.213
- Ligands: GDP.21
22 PLIP interactions:19 interactions with chain D, 3 interactions with chain C- Hydrogen bonds: D:T.168, D:S.169, D:S.169, D:S.169, D:R.170, D:R.170, D:D.171, D:T.187, D:T.187, D:I.191, D:K.211, D:G.212, C:K.210
- Water bridges: D:D.189, D:D.189, D:K.213, D:K.213
- Salt bridges: D:R.170, D:K.211, C:R.170, C:R.170
- pi-Cation interactions: D:K.211
GDP.21: 17 residues within 4Å:- Chain D: K.118, Y.119, E.120, N.121, I.124, P.127, V.128, F.148, A.149, G.150, K.213, M.226, S.228, T.230, D.231, K.234
- Ligands: GDP.20
20 PLIP interactions:20 interactions with chain D- Hydrogen bonds: D:Y.119, D:N.121, D:N.121, D:V.128, D:A.149, D:G.150, D:G.150, D:K.213, D:S.228, D:T.230, D:D.231, D:K.234
- Water bridges: D:K.118, D:A.149, D:G.150, D:S.169
- Salt bridges: D:K.213, D:K.213
- pi-Stacking: D:F.148
- pi-Cation interactions: D:F.148
GDP.22: 14 residues within 4Å:- Chain D: E.120, N.121, G.122, L.199, E.200, N.203, L.227, S.228, D.231, L.232, N.235, P.239, K.243, K.248
10 PLIP interactions:10 interactions with chain D- Hydrogen bonds: D:N.121, D:N.203, D:N.203, D:N.235, D:N.235, D:K.243
- Water bridges: D:N.235, D:N.235, D:P.239
- Salt bridges: D:K.243
GDP.26: 16 residues within 4Å:- Chain E: I.166, I.167, T.168, S.169, R.170, D.171, T.187, D.189, V.190, I.191, K.211, G.212, K.213
- Chain F: R.170, K.210
- Ligands: GDP.27
17 PLIP interactions:14 interactions with chain E, 3 interactions with chain F- Hydrogen bonds: E:T.168, E:S.169, E:S.169, E:D.171, E:T.187, E:T.187, E:I.191, E:K.211, E:G.212
- Water bridges: E:S.169, E:K.213, E:K.213, E:K.213, F:K.211
- Salt bridges: E:D.189, F:R.170, F:R.170
GDP.27: 17 residues within 4Å:- Chain E: K.118, Y.119, E.120, N.121, I.124, P.127, V.128, F.148, A.149, G.150, K.213, M.226, S.228, T.230, D.231, K.234
- Ligands: GDP.26
20 PLIP interactions:20 interactions with chain E- Hydrogen bonds: E:Y.119, E:N.121, E:N.121, E:V.128, E:A.149, E:G.150, E:G.150, E:K.213, E:S.228, E:T.230, E:D.231, E:K.234
- Water bridges: E:K.118, E:G.150, E:S.169, E:T.230
- Salt bridges: E:K.213, E:K.213
- pi-Stacking: E:F.148
- pi-Cation interactions: E:F.148
GDP.28: 14 residues within 4Å:- Chain E: E.120, N.121, G.122, L.199, E.200, N.203, K.207, L.227, S.228, D.231, L.232, N.235, K.243, K.248
10 PLIP interactions:10 interactions with chain E- Hydrogen bonds: E:E.120, E:N.121, E:E.200, E:N.203, E:N.203, E:K.243, E:K.248
- Water bridges: E:N.235
- Salt bridges: E:K.243, E:K.248
GDP.32: 16 residues within 4Å:- Chain E: R.170, K.210
- Chain F: I.166, I.167, T.168, S.169, R.170, D.171, T.187, D.189, V.190, I.191, K.211, G.212, K.213
- Ligands: GDP.33
22 PLIP interactions:19 interactions with chain F, 3 interactions with chain E- Hydrogen bonds: F:T.168, F:S.169, F:S.169, F:S.169, F:R.170, F:R.170, F:D.171, F:T.187, F:T.187, F:I.191, F:K.211, F:G.212, E:K.210
- Water bridges: F:D.189, F:D.189, F:K.213, F:K.213
- Salt bridges: F:R.170, F:K.211, E:R.170, E:R.170
- pi-Cation interactions: F:K.211
GDP.33: 17 residues within 4Å:- Chain F: K.118, Y.119, E.120, N.121, I.124, P.127, V.128, F.148, A.149, G.150, K.213, M.226, S.228, T.230, D.231, K.234
- Ligands: GDP.32
20 PLIP interactions:20 interactions with chain F- Hydrogen bonds: F:Y.119, F:N.121, F:N.121, F:V.128, F:A.149, F:G.150, F:G.150, F:K.213, F:S.228, F:T.230, F:D.231, F:K.234
- Water bridges: F:K.118, F:A.149, F:G.150, F:S.169
- Salt bridges: F:K.213, F:K.213
- pi-Stacking: F:F.148
- pi-Cation interactions: F:F.148
GDP.34: 14 residues within 4Å:- Chain F: E.120, N.121, G.122, L.199, E.200, N.203, L.227, S.228, D.231, L.232, N.235, P.239, K.243, K.248
10 PLIP interactions:10 interactions with chain F- Hydrogen bonds: F:N.121, F:N.203, F:N.203, F:N.235, F:N.235, F:K.243
- Water bridges: F:N.235, F:N.235, F:P.239
- Salt bridges: F:K.243
GDP.38: 16 residues within 4Å:- Chain G: I.166, I.167, T.168, S.169, R.170, D.171, T.187, D.189, V.190, I.191, K.211, G.212, K.213
- Chain H: R.170, K.210
- Ligands: GDP.39
17 PLIP interactions:14 interactions with chain G, 3 interactions with chain H- Hydrogen bonds: G:T.168, G:S.169, G:S.169, G:D.171, G:T.187, G:T.187, G:I.191, G:K.211, G:G.212
- Water bridges: G:S.169, G:K.213, G:K.213, G:K.213, H:K.211
- Salt bridges: G:D.189, H:R.170, H:R.170
GDP.39: 17 residues within 4Å:- Chain G: K.118, Y.119, E.120, N.121, I.124, P.127, V.128, F.148, A.149, G.150, K.213, M.226, S.228, T.230, D.231, K.234
- Ligands: GDP.38
20 PLIP interactions:20 interactions with chain G- Hydrogen bonds: G:Y.119, G:N.121, G:N.121, G:V.128, G:A.149, G:G.150, G:G.150, G:K.213, G:S.228, G:T.230, G:D.231, G:K.234
- Water bridges: G:K.118, G:G.150, G:S.169, G:T.230
- Salt bridges: G:K.213, G:K.213
- pi-Stacking: G:F.148
- pi-Cation interactions: G:F.148
GDP.40: 14 residues within 4Å:- Chain G: E.120, N.121, G.122, L.199, E.200, N.203, K.207, L.227, S.228, D.231, L.232, N.235, K.243, K.248
10 PLIP interactions:10 interactions with chain G- Hydrogen bonds: G:E.120, G:N.121, G:E.200, G:N.203, G:N.203, G:K.243, G:K.248
- Water bridges: G:N.235
- Salt bridges: G:K.243, G:K.248
GDP.44: 16 residues within 4Å:- Chain G: R.170, K.210
- Chain H: I.166, I.167, T.168, S.169, R.170, D.171, T.187, D.189, V.190, I.191, K.211, G.212, K.213
- Ligands: GDP.45
22 PLIP interactions:19 interactions with chain H, 3 interactions with chain G- Hydrogen bonds: H:T.168, H:S.169, H:S.169, H:S.169, H:R.170, H:R.170, H:D.171, H:T.187, H:T.187, H:I.191, H:K.211, H:G.212, G:K.210
- Water bridges: H:D.189, H:D.189, H:K.213, H:K.213
- Salt bridges: H:R.170, H:K.211, G:R.170, G:R.170
- pi-Cation interactions: H:K.211
GDP.45: 17 residues within 4Å:- Chain H: K.118, Y.119, E.120, N.121, I.124, P.127, V.128, F.148, A.149, G.150, K.213, M.226, S.228, T.230, D.231, K.234
- Ligands: GDP.44
20 PLIP interactions:20 interactions with chain H- Hydrogen bonds: H:Y.119, H:N.121, H:N.121, H:V.128, H:A.149, H:G.150, H:G.150, H:K.213, H:S.228, H:T.230, H:D.231, H:K.234
- Water bridges: H:K.118, H:A.149, H:G.150, H:S.169
- Salt bridges: H:K.213, H:K.213
- pi-Stacking: H:F.148
- pi-Cation interactions: H:F.148
GDP.46: 14 residues within 4Å:- Chain H: E.120, N.121, G.122, L.199, E.200, N.203, L.227, S.228, D.231, L.232, N.235, P.239, K.243, K.248
10 PLIP interactions:10 interactions with chain H- Hydrogen bonds: H:N.121, H:N.203, H:N.203, H:N.235, H:N.235, H:K.243
- Water bridges: H:N.235, H:N.235, H:P.239
- Salt bridges: H:K.243
- 8 x K: POTASSIUM ION(Non-covalent)
K.5: 8 residues within 4Å:- Chain A: G.332, S.333, G.334, C.337
- Chain G: E.510, G.511, G.512, H.514
5 PLIP interactions:3 interactions with chain G, 2 interactions with chain A- Metal complexes: G:E.510, G:G.511, G:G.512, A:G.334, A:C.337
K.11: 7 residues within 4Å:- Chain B: G.332, G.334, C.337
- Chain F: E.510, G.511, G.512, H.514
5 PLIP interactions:3 interactions with chain B, 2 interactions with chain F- Metal complexes: B:G.332, B:G.334, B:C.337, F:G.511, F:G.512
K.17: 8 residues within 4Å:- Chain C: G.332, S.333, G.334, C.337
- Chain E: E.510, G.511, G.512, H.514
5 PLIP interactions:3 interactions with chain E, 2 interactions with chain C- Metal complexes: E:E.510, E:G.511, E:G.512, C:G.334, C:C.337
K.23: 7 residues within 4Å:- Chain D: G.332, G.334, C.337
- Chain H: E.510, G.511, G.512, H.514
5 PLIP interactions:2 interactions with chain H, 3 interactions with chain D- Metal complexes: H:G.511, H:G.512, D:G.332, D:G.334, D:C.337
K.29: 8 residues within 4Å:- Chain A: E.510, G.511, G.512, H.514
- Chain E: G.332, S.333, G.334, C.337
5 PLIP interactions:2 interactions with chain E, 3 interactions with chain A- Metal complexes: E:G.334, E:C.337, A:E.510, A:G.511, A:G.512
K.35: 7 residues within 4Å:- Chain D: E.510, G.511, G.512, H.514
- Chain F: G.332, G.334, C.337
5 PLIP interactions:3 interactions with chain F, 2 interactions with chain D- Metal complexes: F:G.332, F:G.334, F:C.337, D:G.511, D:G.512
K.41: 8 residues within 4Å:- Chain C: E.510, G.511, G.512, H.514
- Chain G: G.332, S.333, G.334, C.337
5 PLIP interactions:2 interactions with chain G, 3 interactions with chain C- Metal complexes: G:G.334, G:C.337, C:E.510, C:G.511, C:G.512
K.47: 7 residues within 4Å:- Chain B: E.510, G.511, G.512, H.514
- Chain H: G.332, G.334, C.337
5 PLIP interactions:3 interactions with chain H, 2 interactions with chain B- Metal complexes: H:G.332, H:G.334, H:C.337, B:G.511, B:G.512
- 8 x ACT: ACETATE ION(Non-functional Binders)
ACT.6: 4 residues within 4Å:- Chain A: S.61, T.69, L.70, N.71
1 PLIP interactions:1 interactions with chain A- Hydrophobic interactions: A:T.69
ACT.12: 5 residues within 4Å:- Chain B: L.94, L.240, I.467, P.468, Y.471
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:Y.471
ACT.18: 4 residues within 4Å:- Chain C: S.61, T.69, L.70, N.71
1 PLIP interactions:1 interactions with chain C- Hydrophobic interactions: C:T.69
ACT.24: 5 residues within 4Å:- Chain D: L.94, L.240, I.467, P.468, Y.471
1 PLIP interactions:1 interactions with chain D- Hydrophobic interactions: D:Y.471
ACT.30: 4 residues within 4Å:- Chain E: S.61, T.69, L.70, N.71
1 PLIP interactions:1 interactions with chain E- Hydrophobic interactions: E:T.69
ACT.36: 5 residues within 4Å:- Chain F: L.94, L.240, I.467, P.468, Y.471
1 PLIP interactions:1 interactions with chain F- Hydrophobic interactions: F:Y.471
ACT.42: 4 residues within 4Å:- Chain G: S.61, T.69, L.70, N.71
1 PLIP interactions:1 interactions with chain G- Hydrophobic interactions: G:T.69
ACT.48: 5 residues within 4Å:- Chain H: L.94, L.240, I.467, P.468, Y.471
1 PLIP interactions:1 interactions with chain H- Hydrophobic interactions: H:Y.471
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Buey, R.M. et al., Guanine nucleotide binding to the Bateman domain mediates the allosteric inhibition of eukaryotic IMP dehydrogenases. Nat Commun (2015)
- Release Date
- 2015-11-25
- Peptides
- Inosine-5'-monophosphate dehydrogenase: ABCDEFGH
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
BE
AF
BG
AH
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.25 Å
- Oligo State
- homo-octamer
- Ligands
- 8 x 5GP: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)
- 24 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)
- 8 x K: POTASSIUM ION(Non-covalent)
- 8 x ACT: ACETATE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Buey, R.M. et al., Guanine nucleotide binding to the Bateman domain mediates the allosteric inhibition of eukaryotic IMP dehydrogenases. Nat Commun (2015)
- Release Date
- 2015-11-25
- Peptides
- Inosine-5'-monophosphate dehydrogenase: ABCDEFGH
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
BE
AF
BG
AH
B