- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.20 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x VNR: 1-deoxy-1-[(4aR)-4a-[(2Z)-2-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)but-2-en-1-yl]-7,8-dimethyl-2,4-dioxo-3,4,4a,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-5-O-phosphono-D-ribitol(Non-covalent)
VNR.1: 30 residues within 4Å:- Chain A: R.7, K.8, H.11, A.15, T.65, G.66, M.67, G.95, S.96, R.98, N.125, Q.130, H.155, N.157, Q.160, E.161, K.193, E.194, S.195, S.218, G.222, T.223, W.225, G.274, G.275, R.277, M.295, A.296, L.297
- Ligands: MG.2
37 PLIP interactions:37 interactions with chain A- Hydrophobic interactions: A:A.15, A:M.67, A:N.157
- Hydrogen bonds: A:T.65, A:G.66, A:M.67, A:S.96, A:S.96, A:N.125, A:N.125, A:Q.130, A:N.157, A:Q.160, A:K.193, A:K.193, A:S.218, A:T.223, A:T.223, A:W.225, A:G.274, A:G.275, A:A.296, A:L.297
- Water bridges: A:G.222, A:S.273, A:R.277, A:R.277
- Salt bridges: A:R.7, A:R.7, A:K.8, A:K.8, A:H.11, A:R.98, A:H.155, A:R.277
- pi-Stacking: A:W.225, A:W.225
VNR.3: 30 residues within 4Å:- Chain B: R.7, K.8, H.11, A.15, T.65, G.66, M.67, G.95, S.96, R.98, N.125, Q.130, H.155, N.157, Q.160, E.161, Q.164, K.193, E.194, S.195, S.218, G.222, T.223, W.225, G.274, G.275, R.277, M.295, A.296, L.297
36 PLIP interactions:36 interactions with chain B- Hydrophobic interactions: B:A.15, B:M.67, B:N.157, B:W.225
- Hydrogen bonds: B:T.65, B:G.66, B:M.67, B:S.96, B:S.96, B:N.125, B:N.125, B:Q.130, B:N.157, B:Q.160, B:K.193, B:K.193, B:T.223, B:T.223, B:W.225, B:G.274, B:G.275, B:A.296, B:L.297
- Water bridges: B:G.222, B:S.273, B:I.276, B:R.277
- Salt bridges: B:R.7, B:R.7, B:K.8, B:K.8, B:H.11, B:R.98, B:R.277
- pi-Stacking: B:W.225, B:W.225
VNR.5: 32 residues within 4Å:- Chain C: I.4, R.7, K.8, H.11, A.15, T.65, G.66, M.67, G.95, S.96, R.98, N.125, Q.130, H.155, N.157, Q.160, E.161, Q.164, K.193, E.194, S.195, S.218, G.222, T.223, W.225, G.274, G.275, R.277, M.295, A.296, L.297
- Ligands: MG.4
35 PLIP interactions:35 interactions with chain C- Hydrophobic interactions: C:A.15, C:M.67, C:N.157, C:T.223, C:W.225
- Hydrogen bonds: C:T.65, C:G.66, C:M.67, C:S.96, C:S.96, C:N.125, C:N.125, C:Q.130, C:N.157, C:Q.160, C:K.193, C:K.193, C:T.223, C:T.223, C:W.225, C:G.274, C:G.275, C:A.296, C:L.297
- Water bridges: C:G.222, C:I.276, C:R.277
- Salt bridges: C:R.7, C:R.7, C:K.8, C:K.8, C:H.11, C:R.98, C:R.277
- pi-Stacking: C:W.225
VNR.7: 31 residues within 4Å:- Chain D: R.7, K.8, H.11, A.15, T.65, G.66, M.67, G.95, S.96, R.98, N.125, Q.130, H.155, N.157, Q.160, E.161, K.193, E.194, S.195, S.218, G.222, T.223, W.225, G.274, G.275, R.277, M.295, A.296, L.297, L.300
- Ligands: MG.6
40 PLIP interactions:40 interactions with chain D- Hydrophobic interactions: D:A.15, D:M.67, D:N.157, D:T.223, D:L.300
- Hydrogen bonds: D:T.65, D:G.66, D:M.67, D:S.96, D:S.96, D:N.125, D:N.125, D:Q.130, D:N.157, D:Q.160, D:K.193, D:K.193, D:S.218, D:T.223, D:T.223, D:W.225, D:G.274, D:G.275, D:A.296, D:L.297
- Water bridges: D:K.8, D:R.98, D:Q.164, D:G.222, D:S.273, D:I.276, D:R.277
- Salt bridges: D:R.7, D:R.7, D:K.8, D:K.8, D:H.11, D:R.98, D:R.277
- pi-Stacking: D:W.225
- 3 x MG: MAGNESIUM ION(Non-covalent)
MG.2: 4 residues within 4Å:- Chain A: H.155, N.157, E.161
- Ligands: VNR.1
No protein-ligand interaction detected (PLIP)MG.4: 4 residues within 4Å:- Chain C: R.98, N.157, E.161
- Ligands: VNR.5
1 PLIP interactions:1 interactions with chain C- Metal complexes: C:E.161
MG.6: 4 residues within 4Å:- Chain D: R.98, N.157, E.161
- Ligands: VNR.7
3 PLIP interactions:1 interactions with chain D, 2 Ligand-Water interactions- Metal complexes: D:E.161, H2O.19, H2O.21
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Nagai, T. et al., Covalent modification of reduced flavin mononucleotide in type-2 isopentenyl diphosphate isomerase by active-site-directed inhibitors. Proc.Natl.Acad.Sci.USA (2011)
- Release Date
- 2011-11-02
- Peptides
- Isopentenyl-diphosphate delta-isomerase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.20 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x VNR: 1-deoxy-1-[(4aR)-4a-[(2Z)-2-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)but-2-en-1-yl]-7,8-dimethyl-2,4-dioxo-3,4,4a,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-5-O-phosphono-D-ribitol(Non-covalent)
- 3 x MG: MAGNESIUM ION(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Nagai, T. et al., Covalent modification of reduced flavin mononucleotide in type-2 isopentenyl diphosphate isomerase by active-site-directed inhibitors. Proc.Natl.Acad.Sci.USA (2011)
- Release Date
- 2011-11-02
- Peptides
- Isopentenyl-diphosphate delta-isomerase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D