- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.65 Å
- Oligo State
- homo-octamer
- Ligands
- 8 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
- 8 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)
GDP.2: 20 residues within 4Å:- Chain A: K.91, H.92, E.93, T.94, V.97, P.100, V.101, F.121, S.122, G.123, F.124, P.125, K.184, L.197, T.199, R.201, D.202, K.205
- Ligands: ATP.1, MG.4
22 PLIP interactions:22 interactions with chain A- Hydrogen bonds: A:K.91, A:V.101, A:S.122, A:G.123, A:G.123, A:G.123, A:D.202, A:D.202
- Water bridges: A:E.183, A:K.184, A:K.184, A:K.184, A:K.184, A:K.184, A:R.201, A:R.201
- Salt bridges: A:K.184, A:K.184, A:R.201, A:R.201
- pi-Stacking: A:F.121
- pi-Cation interactions: A:F.121
GDP.9: 20 residues within 4Å:- Chain B: K.91, H.92, E.93, T.94, V.97, P.100, V.101, F.121, S.122, G.123, F.124, P.125, K.184, L.197, T.199, R.201, D.202, K.205
- Ligands: ATP.8, MG.11
22 PLIP interactions:22 interactions with chain B- Hydrogen bonds: B:K.91, B:V.101, B:S.122, B:G.123, B:G.123, B:G.123, B:D.202, B:D.202
- Water bridges: B:E.183, B:K.184, B:K.184, B:K.184, B:K.184, B:K.184, B:R.201, B:R.201
- Salt bridges: B:K.184, B:K.184, B:R.201, B:R.201
- pi-Stacking: B:F.121
- pi-Cation interactions: B:F.121
GDP.16: 20 residues within 4Å:- Chain C: K.91, H.92, E.93, T.94, V.97, P.100, V.101, F.121, S.122, G.123, F.124, P.125, K.184, L.197, T.199, R.201, D.202, K.205
- Ligands: ATP.15, MG.18
22 PLIP interactions:22 interactions with chain C- Hydrogen bonds: C:K.91, C:V.101, C:S.122, C:G.123, C:G.123, C:G.123, C:D.202, C:D.202
- Water bridges: C:E.183, C:K.184, C:K.184, C:K.184, C:K.184, C:K.184, C:R.201, C:R.201
- Salt bridges: C:K.184, C:K.184, C:R.201, C:R.201
- pi-Stacking: C:F.121
- pi-Cation interactions: C:F.121
GDP.23: 20 residues within 4Å:- Chain D: K.91, H.92, E.93, T.94, V.97, P.100, V.101, F.121, S.122, G.123, F.124, P.125, K.184, L.197, T.199, R.201, D.202, K.205
- Ligands: ATP.22, MG.25
22 PLIP interactions:22 interactions with chain D- Hydrogen bonds: D:K.91, D:V.101, D:S.122, D:G.123, D:G.123, D:G.123, D:D.202, D:D.202
- Water bridges: D:E.183, D:K.184, D:K.184, D:K.184, D:K.184, D:K.184, D:R.201, D:R.201
- Salt bridges: D:K.184, D:K.184, D:R.201, D:R.201
- pi-Stacking: D:F.121
- pi-Cation interactions: D:F.121
GDP.30: 19 residues within 4Å:- Chain E: K.91, H.92, E.93, T.94, V.97, P.100, V.101, F.121, S.122, G.123, P.125, K.184, L.197, T.199, R.201, D.202, K.205
- Ligands: ATP.29, MG.32
27 PLIP interactions:27 interactions with chain E- Hydrogen bonds: E:K.91, E:V.101, E:S.122, E:G.123, E:G.123, E:G.123, E:D.202, E:D.202, E:K.205
- Water bridges: E:S.122, E:E.183, E:E.183, E:K.184, E:K.184, E:K.184, E:K.184, E:K.184, E:K.184, E:R.201, E:R.201, E:R.201
- Salt bridges: E:K.184, E:K.184, E:R.201, E:R.201
- pi-Stacking: E:F.121
- pi-Cation interactions: E:F.121
GDP.37: 19 residues within 4Å:- Chain F: K.91, H.92, E.93, T.94, V.97, P.100, V.101, F.121, S.122, G.123, P.125, K.184, L.197, T.199, R.201, D.202, K.205
- Ligands: ATP.36, MG.39
27 PLIP interactions:27 interactions with chain F- Hydrogen bonds: F:K.91, F:V.101, F:S.122, F:G.123, F:G.123, F:G.123, F:D.202, F:D.202, F:K.205
- Water bridges: F:S.122, F:E.183, F:E.183, F:K.184, F:K.184, F:K.184, F:K.184, F:K.184, F:K.184, F:R.201, F:R.201, F:R.201
- Salt bridges: F:K.184, F:K.184, F:R.201, F:R.201
- pi-Stacking: F:F.121
- pi-Cation interactions: F:F.121
GDP.44: 19 residues within 4Å:- Chain G: K.91, H.92, E.93, T.94, V.97, P.100, V.101, F.121, S.122, G.123, P.125, K.184, L.197, T.199, R.201, D.202, K.205
- Ligands: ATP.43, MG.46
27 PLIP interactions:27 interactions with chain G- Hydrogen bonds: G:K.91, G:V.101, G:S.122, G:G.123, G:G.123, G:G.123, G:D.202, G:D.202, G:K.205
- Water bridges: G:S.122, G:E.183, G:E.183, G:K.184, G:K.184, G:K.184, G:K.184, G:K.184, G:K.184, G:R.201, G:R.201, G:R.201
- Salt bridges: G:K.184, G:K.184, G:R.201, G:R.201
- pi-Stacking: G:F.121
- pi-Cation interactions: G:F.121
GDP.51: 19 residues within 4Å:- Chain H: K.91, H.92, E.93, T.94, V.97, P.100, V.101, F.121, S.122, G.123, P.125, K.184, L.197, T.199, R.201, D.202, K.205
- Ligands: ATP.50, MG.53
27 PLIP interactions:27 interactions with chain H- Hydrogen bonds: H:K.91, H:V.101, H:S.122, H:G.123, H:G.123, H:G.123, H:D.202, H:D.202, H:K.205
- Water bridges: H:S.122, H:E.183, H:E.183, H:K.184, H:K.184, H:K.184, H:K.184, H:K.184, H:K.184, H:R.201, H:R.201, H:R.201
- Salt bridges: H:K.184, H:K.184, H:R.201, H:R.201
- pi-Stacking: H:F.121
- pi-Cation interactions: H:F.121
- 8 x IMP: INOSINIC ACID(Non-covalent)
IMP.3: 24 residues within 4Å:- Chain A: A.50, M.52, N.279, K.298, G.304, S.305, I.306, C.307, T.308, T.309, D.340, G.341, G.342, I.343, M.361, M.362, G.363, S.364, Y.387, G.389, M.390, E.420, G.421
- Chain D: H.478
18 PLIP interactions:18 interactions with chain A- Hydrogen bonds: A:N.279, A:S.305, A:T.309, A:D.340, A:G.342, A:G.363, A:S.364, A:Y.387, A:M.390, A:E.420
- Water bridges: A:G.300, A:G.302, A:G.304, A:D.340, A:I.343, A:I.343, A:I.343, A:M.365
IMP.10: 24 residues within 4Å:- Chain B: A.50, M.52, N.279, K.298, G.304, S.305, I.306, C.307, T.308, T.309, D.340, G.341, G.342, I.343, M.361, M.362, G.363, S.364, Y.387, G.389, M.390, E.420, G.421
- Chain C: H.478
18 PLIP interactions:18 interactions with chain B- Hydrogen bonds: B:N.279, B:S.305, B:T.309, B:D.340, B:G.342, B:G.363, B:S.364, B:Y.387, B:M.390, B:E.420
- Water bridges: B:G.300, B:G.302, B:G.304, B:D.340, B:I.343, B:I.343, B:I.343, B:M.365
IMP.17: 24 residues within 4Å:- Chain A: H.478
- Chain C: A.50, M.52, N.279, K.298, G.304, S.305, I.306, C.307, T.308, T.309, D.340, G.341, G.342, I.343, M.361, M.362, G.363, S.364, Y.387, G.389, M.390, E.420, G.421
18 PLIP interactions:18 interactions with chain C- Hydrogen bonds: C:N.279, C:S.305, C:T.309, C:D.340, C:G.342, C:G.363, C:S.364, C:Y.387, C:M.390, C:E.420
- Water bridges: C:G.300, C:G.302, C:G.304, C:D.340, C:I.343, C:I.343, C:I.343, C:M.365
IMP.24: 24 residues within 4Å:- Chain B: H.478
- Chain D: A.50, M.52, N.279, K.298, G.304, S.305, I.306, C.307, T.308, T.309, D.340, G.341, G.342, I.343, M.361, M.362, G.363, S.364, Y.387, G.389, M.390, E.420, G.421
18 PLIP interactions:18 interactions with chain D- Hydrogen bonds: D:N.279, D:S.305, D:T.309, D:D.340, D:G.342, D:G.363, D:S.364, D:Y.387, D:M.390, D:E.420
- Water bridges: D:G.300, D:G.302, D:G.304, D:D.340, D:I.343, D:I.343, D:I.343, D:M.365
IMP.31: 24 residues within 4Å:- Chain E: A.50, M.52, N.279, K.298, G.304, S.305, I.306, C.307, T.308, T.309, D.340, G.341, G.342, I.343, M.361, M.362, G.363, S.364, Y.387, G.389, M.390, G.391, E.420, G.421
18 PLIP interactions:18 interactions with chain E- Hydrogen bonds: E:N.279, E:S.305, E:S.305, E:D.340, E:G.342, E:G.363, E:S.364, E:Y.387, E:M.390, E:G.391, E:E.420
- Water bridges: E:G.300, E:G.302, E:G.304, E:D.340, E:G.341, E:S.364, E:M.365
IMP.38: 24 residues within 4Å:- Chain F: A.50, M.52, N.279, K.298, G.304, S.305, I.306, C.307, T.308, T.309, D.340, G.341, G.342, I.343, M.361, M.362, G.363, S.364, Y.387, G.389, M.390, G.391, E.420, G.421
18 PLIP interactions:18 interactions with chain F- Hydrogen bonds: F:N.279, F:S.305, F:S.305, F:D.340, F:G.342, F:G.363, F:S.364, F:Y.387, F:M.390, F:G.391, F:E.420
- Water bridges: F:G.300, F:G.302, F:G.304, F:D.340, F:G.341, F:S.364, F:M.365
IMP.45: 24 residues within 4Å:- Chain G: A.50, M.52, N.279, K.298, G.304, S.305, I.306, C.307, T.308, T.309, D.340, G.341, G.342, I.343, M.361, M.362, G.363, S.364, Y.387, G.389, M.390, G.391, E.420, G.421
18 PLIP interactions:18 interactions with chain G- Hydrogen bonds: G:N.279, G:S.305, G:S.305, G:D.340, G:G.342, G:G.363, G:S.364, G:Y.387, G:M.390, G:G.391, G:E.420
- Water bridges: G:G.300, G:G.302, G:G.304, G:D.340, G:G.341, G:S.364, G:M.365
IMP.52: 24 residues within 4Å:- Chain H: A.50, M.52, N.279, K.298, G.304, S.305, I.306, C.307, T.308, T.309, D.340, G.341, G.342, I.343, M.361, M.362, G.363, S.364, Y.387, G.389, M.390, G.391, E.420, G.421
18 PLIP interactions:18 interactions with chain H- Hydrogen bonds: H:N.279, H:S.305, H:S.305, H:D.340, H:G.342, H:G.363, H:S.364, H:Y.387, H:M.390, H:G.391, H:E.420
- Water bridges: H:G.300, H:G.302, H:G.304, H:D.340, H:G.341, H:S.364, H:M.365
- 8 x MG: MAGNESIUM ION(Non-covalent)
MG.4: 3 residues within 4Å:- Chain A: K.184
- Ligands: ATP.1, GDP.2
No protein-ligand interaction detected (PLIP)MG.11: 3 residues within 4Å:- Chain B: K.184
- Ligands: ATP.8, GDP.9
No protein-ligand interaction detected (PLIP)MG.18: 3 residues within 4Å:- Chain C: K.184
- Ligands: ATP.15, GDP.16
No protein-ligand interaction detected (PLIP)MG.25: 3 residues within 4Å:- Chain D: K.184
- Ligands: ATP.22, GDP.23
No protein-ligand interaction detected (PLIP)MG.32: 3 residues within 4Å:- Chain E: K.184
- Ligands: ATP.29, GDP.30
No protein-ligand interaction detected (PLIP)MG.39: 3 residues within 4Å:- Chain F: K.184
- Ligands: ATP.36, GDP.37
No protein-ligand interaction detected (PLIP)MG.46: 3 residues within 4Å:- Chain G: K.184
- Ligands: ATP.43, GDP.44
No protein-ligand interaction detected (PLIP)MG.53: 3 residues within 4Å:- Chain H: K.184
- Ligands: ATP.50, GDP.51
No protein-ligand interaction detected (PLIP)- 8 x K: POTASSIUM ION(Non-covalent)
K.5: 9 residues within 4Å:- Chain A: G.302, P.303, G.304, C.307
- Chain D: E.474, S.475, H.476, V.477, H.478
5 PLIP interactions:3 interactions with chain A, 2 interactions with chain D- Metal complexes: A:G.302, A:G.304, A:C.307, D:E.474, D:S.475
K.12: 9 residues within 4Å:- Chain B: G.302, P.303, G.304, C.307
- Chain C: E.474, S.475, H.476, V.477, H.478
5 PLIP interactions:3 interactions with chain B, 2 interactions with chain C- Metal complexes: B:G.302, B:G.304, B:C.307, C:E.474, C:S.475
K.19: 9 residues within 4Å:- Chain A: E.474, S.475, H.476, V.477, H.478
- Chain C: G.302, P.303, G.304, C.307
5 PLIP interactions:2 interactions with chain A, 3 interactions with chain C- Metal complexes: A:E.474, A:S.475, C:G.302, C:G.304, C:C.307
K.26: 9 residues within 4Å:- Chain B: E.474, S.475, H.476, V.477, H.478
- Chain D: G.302, P.303, G.304, C.307
5 PLIP interactions:2 interactions with chain B, 3 interactions with chain D- Metal complexes: B:E.474, B:S.475, D:G.302, D:G.304, D:C.307
K.33: 8 residues within 4Å:- Chain E: G.302, P.303, G.304, C.307
- Chain G: E.474, S.475, H.476, H.478
5 PLIP interactions:3 interactions with chain E, 2 interactions with chain G- Metal complexes: E:G.302, E:G.304, E:C.307, G:E.474, G:S.475
K.40: 8 residues within 4Å:- Chain F: G.302, P.303, G.304, C.307
- Chain H: E.474, S.475, H.476, H.478
5 PLIP interactions:3 interactions with chain F, 2 interactions with chain H- Metal complexes: F:G.302, F:G.304, F:C.307, H:E.474, H:S.475
K.47: 8 residues within 4Å:- Chain F: E.474, S.475, H.476, H.478
- Chain G: G.302, P.303, G.304, C.307
5 PLIP interactions:3 interactions with chain G, 2 interactions with chain F- Metal complexes: G:G.302, G:G.304, G:C.307, F:E.474, F:S.475
K.54: 8 residues within 4Å:- Chain E: E.474, S.475, H.476, H.478
- Chain H: G.302, P.303, G.304, C.307
5 PLIP interactions:3 interactions with chain H, 2 interactions with chain E- Metal complexes: H:G.302, H:G.304, H:C.307, E:E.474, E:S.475
- 16 x ACT: ACETATE ION(Non-functional Binders)
ACT.6: 7 residues within 4Å:- Chain A: A.252, H.253, E.420
- Chain D: P.28, A.445, G.448, Y.449
Ligand excluded by PLIPACT.7: 4 residues within 4Å:- Chain A: N.76, M.77, G.78, R.235
Ligand excluded by PLIPACT.13: 7 residues within 4Å:- Chain B: A.252, H.253, E.420
- Chain C: P.28, A.445, G.448, Y.449
Ligand excluded by PLIPACT.14: 4 residues within 4Å:- Chain B: N.76, M.77, G.78, R.235
Ligand excluded by PLIPACT.20: 7 residues within 4Å:- Chain A: P.28, A.445, G.448, Y.449
- Chain C: A.252, H.253, E.420
Ligand excluded by PLIPACT.21: 4 residues within 4Å:- Chain C: N.76, M.77, G.78, R.235
Ligand excluded by PLIPACT.27: 7 residues within 4Å:- Chain B: P.28, A.445, G.448, Y.449
- Chain D: A.252, H.253, E.420
Ligand excluded by PLIPACT.28: 4 residues within 4Å:- Chain D: N.76, M.77, G.78, R.235
Ligand excluded by PLIPACT.34: 7 residues within 4Å:- Chain E: A.252, H.253
- Chain G: L.27, P.28, A.445, G.448, Y.449
Ligand excluded by PLIPACT.35: 5 residues within 4Å:- Chain E: K.75, N.76, M.77, G.78, R.235
Ligand excluded by PLIPACT.41: 7 residues within 4Å:- Chain F: A.252, H.253
- Chain H: L.27, P.28, A.445, G.448, Y.449
Ligand excluded by PLIPACT.42: 5 residues within 4Å:- Chain F: K.75, N.76, M.77, G.78, R.235
Ligand excluded by PLIPACT.48: 7 residues within 4Å:- Chain F: L.27, P.28, A.445, G.448, Y.449
- Chain G: A.252, H.253
Ligand excluded by PLIPACT.49: 5 residues within 4Å:- Chain G: K.75, N.76, M.77, G.78, R.235
Ligand excluded by PLIPACT.55: 7 residues within 4Å:- Chain E: L.27, P.28, A.445, G.448, Y.449
- Chain H: A.252, H.253
Ligand excluded by PLIPACT.56: 5 residues within 4Å:- Chain H: K.75, N.76, M.77, G.78, R.235
Ligand excluded by PLIP- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Fernandez-Justel, D. et al., Diversity of mechanisms to control bacterial GTP homeostasis by the mutually exclusive binding of adenine and guanine nucleotides to IMP dehydrogenase. Protein Sci. (2022)
- Release Date
- 2022-07-06
- Peptides
- Inosine-5'-monophosphate dehydrogenase: ABCDEFGH
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
AD
AE
BF
BG
BH
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.65 Å
- Oligo State
- homo-octamer
- Ligands
- 8 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
- 8 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)
- 8 x IMP: INOSINIC ACID(Non-covalent)
- 8 x MG: MAGNESIUM ION(Non-covalent)
- 8 x K: POTASSIUM ION(Non-covalent)
- 16 x ACT: ACETATE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Fernandez-Justel, D. et al., Diversity of mechanisms to control bacterial GTP homeostasis by the mutually exclusive binding of adenine and guanine nucleotides to IMP dehydrogenase. Protein Sci. (2022)
- Release Date
- 2022-07-06
- Peptides
- Inosine-5'-monophosphate dehydrogenase: ABCDEFGH
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
AD
AE
BF
BG
BH
B