- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.80 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x FLC: CITRATE ANION(Non-covalent)
- 24 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
MPD.2: 5 residues within 4Å:- Chain A: E.158
- Chain B: F.6, Y.144, R.147, A.148
Ligand excluded by PLIPMPD.3: 5 residues within 4Å:- Chain A: V.311, V.312, Y.315, G.316, D.359
Ligand excluded by PLIPMPD.6: 5 residues within 4Å:- Chain A: R.151, A.156, Y.171, L.500
- Ligands: MPD.16
Ligand excluded by PLIPMPD.10: 6 residues within 4Å:- Chain A: F.6, Y.144, R.147, A.148, L.500
- Chain B: E.158
Ligand excluded by PLIPMPD.11: 3 residues within 4Å:- Chain B: E.263, E.416
- Ligands: MRD.4
Ligand excluded by PLIPMPD.12: 3 residues within 4Å:- Chain B: P.353, E.355, E.356
Ligand excluded by PLIPMPD.13: 3 residues within 4Å:- Chain A: L.262, E.416
- Ligands: MRD.14
Ligand excluded by PLIPMPD.16: 6 residues within 4Å:- Chain B: R.151, Y.152, A.156, Y.171, L.500
- Ligands: MPD.6
Ligand excluded by PLIPMPD.21: 5 residues within 4Å:- Chain C: E.158
- Chain D: F.6, Y.144, R.147, A.148
Ligand excluded by PLIPMPD.22: 5 residues within 4Å:- Chain C: V.311, V.312, Y.315, G.316, D.359
Ligand excluded by PLIPMPD.25: 5 residues within 4Å:- Chain C: R.151, A.156, Y.171, L.500
- Ligands: MPD.35
Ligand excluded by PLIPMPD.29: 6 residues within 4Å:- Chain C: F.6, Y.144, R.147, A.148, L.500
- Chain D: E.158
Ligand excluded by PLIPMPD.30: 3 residues within 4Å:- Chain D: E.263, E.416
- Ligands: MRD.23
Ligand excluded by PLIPMPD.31: 3 residues within 4Å:- Chain D: P.353, E.355, E.356
Ligand excluded by PLIPMPD.32: 3 residues within 4Å:- Chain C: L.262, E.416
- Ligands: MRD.33
Ligand excluded by PLIPMPD.35: 6 residues within 4Å:- Chain D: R.151, Y.152, A.156, Y.171, L.500
- Ligands: MPD.25
Ligand excluded by PLIPMPD.40: 5 residues within 4Å:- Chain E: E.158
- Chain F: F.6, Y.144, R.147, A.148
Ligand excluded by PLIPMPD.41: 5 residues within 4Å:- Chain E: V.311, V.312, Y.315, G.316, D.359
Ligand excluded by PLIPMPD.44: 5 residues within 4Å:- Chain E: R.151, A.156, Y.171, L.500
- Ligands: MPD.54
Ligand excluded by PLIPMPD.48: 6 residues within 4Å:- Chain E: F.6, Y.144, R.147, A.148, L.500
- Chain F: E.158
Ligand excluded by PLIPMPD.49: 3 residues within 4Å:- Chain F: E.263, E.416
- Ligands: MRD.42
Ligand excluded by PLIPMPD.50: 3 residues within 4Å:- Chain F: P.353, E.355, E.356
Ligand excluded by PLIPMPD.51: 3 residues within 4Å:- Chain E: L.262, E.416
- Ligands: MRD.52
Ligand excluded by PLIPMPD.54: 6 residues within 4Å:- Chain F: R.151, Y.152, A.156, Y.171, L.500
- Ligands: MPD.44
Ligand excluded by PLIP- 15 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)
MRD.4: 7 residues within 4Å:- Chain A: L.275, G.278, Q.279, T.280
- Chain B: P.442, L.490
- Ligands: MPD.11
4 PLIP interactions:3 interactions with chain A, 1 interactions with chain B- Hydrophobic interactions: A:L.275, A:T.280, B:P.442
- Hydrogen bonds: A:G.278
MRD.5: 6 residues within 4Å:- Chain A: I.180, E.241, G.244, A.245, V.264, I.268
8 PLIP interactions:8 interactions with chain A- Hydrophobic interactions: A:I.180, A:E.241, A:A.245, A:V.264, A:I.268
- Hydrogen bonds: A:E.241, A:A.245
- Water bridges: A:G.244
MRD.14: 5 residues within 4Å:- Chain A: P.442
- Chain B: L.275, G.278, Q.279
- Ligands: MPD.13
3 PLIP interactions:1 interactions with chain A, 2 interactions with chain B- Hydrophobic interactions: A:P.442, B:L.275
- Hydrogen bonds: B:G.278
MRD.15: 5 residues within 4Å:- Chain B: I.180, E.241, G.244, A.245, I.268
5 PLIP interactions:5 interactions with chain B- Hydrophobic interactions: B:I.180, B:I.268
- Hydrogen bonds: B:E.241, B:A.245
- Water bridges: B:G.244
MRD.17: 6 residues within 4Å:- Chain B: E.4, P.5, R.7, R.110, E.143, R.147
8 PLIP interactions:8 interactions with chain B- Hydrophobic interactions: B:E.4, B:E.143
- Hydrogen bonds: B:R.147
- Water bridges: B:E.4, B:E.4, B:R.110, B:E.143, B:E.143
MRD.23: 7 residues within 4Å:- Chain C: L.275, G.278, Q.279, T.280
- Chain D: P.442, L.490
- Ligands: MPD.30
4 PLIP interactions:3 interactions with chain C, 1 interactions with chain D- Hydrophobic interactions: C:L.275, C:T.280, D:P.442
- Hydrogen bonds: C:G.278
MRD.24: 6 residues within 4Å:- Chain C: I.180, E.241, G.244, A.245, V.264, I.268
8 PLIP interactions:8 interactions with chain C- Hydrophobic interactions: C:I.180, C:E.241, C:A.245, C:V.264, C:I.268
- Hydrogen bonds: C:E.241, C:A.245
- Water bridges: C:G.244
MRD.33: 5 residues within 4Å:- Chain C: P.442
- Chain D: L.275, G.278, Q.279
- Ligands: MPD.32
3 PLIP interactions:2 interactions with chain D, 1 interactions with chain C- Hydrophobic interactions: D:L.275, C:P.442
- Hydrogen bonds: D:G.278
MRD.34: 5 residues within 4Å:- Chain D: I.180, E.241, G.244, A.245, I.268
5 PLIP interactions:5 interactions with chain D- Hydrophobic interactions: D:I.180, D:I.268
- Hydrogen bonds: D:E.241, D:A.245
- Water bridges: D:G.244
MRD.36: 6 residues within 4Å:- Chain D: E.4, P.5, R.7, R.110, E.143, R.147
8 PLIP interactions:8 interactions with chain D- Hydrophobic interactions: D:E.4, D:E.143
- Hydrogen bonds: D:R.147
- Water bridges: D:E.4, D:E.4, D:R.110, D:E.143, D:E.143
MRD.42: 7 residues within 4Å:- Chain E: L.275, G.278, Q.279, T.280
- Chain F: P.442, L.490
- Ligands: MPD.49
4 PLIP interactions:3 interactions with chain E, 1 interactions with chain F- Hydrophobic interactions: E:L.275, E:T.280, F:P.442
- Hydrogen bonds: E:G.278
MRD.43: 6 residues within 4Å:- Chain E: I.180, E.241, G.244, A.245, V.264, I.268
8 PLIP interactions:8 interactions with chain E- Hydrophobic interactions: E:I.180, E:E.241, E:A.245, E:V.264, E:I.268
- Hydrogen bonds: E:E.241, E:A.245
- Water bridges: E:G.244
MRD.52: 5 residues within 4Å:- Chain E: P.442
- Chain F: L.275, G.278, Q.279
- Ligands: MPD.51
3 PLIP interactions:2 interactions with chain F, 1 interactions with chain E- Hydrophobic interactions: F:L.275, E:P.442
- Hydrogen bonds: F:G.278
MRD.53: 5 residues within 4Å:- Chain F: I.180, E.241, G.244, A.245, I.268
5 PLIP interactions:5 interactions with chain F- Hydrophobic interactions: F:I.180, F:I.268
- Hydrogen bonds: F:E.241, F:A.245
- Water bridges: F:G.244
MRD.55: 6 residues within 4Å:- Chain F: E.4, P.5, R.7, R.110, E.143, R.147
8 PLIP interactions:8 interactions with chain F- Hydrophobic interactions: F:E.4, F:E.143
- Hydrogen bonds: F:R.147
- Water bridges: F:E.4, F:E.4, F:R.110, F:E.143, F:E.143
- 6 x NA: SODIUM ION(Non-functional Binders)
NA.7: 4 residues within 4Å:- Chain A: S.55, L.56, E.123, D.211
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:L.56, A:E.123
NA.18: 4 residues within 4Å:- Chain B: S.55, L.56, E.123, D.211
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:L.56, B:E.123
NA.26: 4 residues within 4Å:- Chain C: S.55, L.56, E.123, D.211
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:L.56, C:L.56
NA.37: 4 residues within 4Å:- Chain D: S.55, L.56, E.123, D.211
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:L.56, D:D.211
NA.45: 4 residues within 4Å:- Chain E: S.55, L.56, E.123, D.211
2 PLIP interactions:2 interactions with chain E- Hydrogen bonds: E:L.56, E:E.123
NA.56: 4 residues within 4Å:- Chain F: S.55, L.56, E.123, D.211
2 PLIP interactions:2 interactions with chain F- Hydrogen bonds: F:S.55, F:L.56
- 6 x CL: CHLORIDE ION(Non-functional Binders)
CL.8: 4 residues within 4Å:- Chain A: K.510
- Chain B: R.462, H.465, F.488
Ligand excluded by PLIPCL.19: 4 residues within 4Å:- Chain A: R.462, H.465, F.488
- Chain B: K.510
Ligand excluded by PLIPCL.27: 4 residues within 4Å:- Chain C: K.510
- Chain D: R.462, H.465, F.488
Ligand excluded by PLIPCL.38: 4 residues within 4Å:- Chain C: R.462, H.465, F.488
- Chain D: K.510
Ligand excluded by PLIPCL.46: 4 residues within 4Å:- Chain E: K.510
- Chain F: R.462, H.465, F.488
Ligand excluded by PLIPCL.57: 4 residues within 4Å:- Chain E: R.462, H.465, F.488
- Chain F: K.510
Ligand excluded by PLIP- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Inagaki, E. et al., Crystal Structure of Thermus Thermophilus Delta(1)- Pyrroline-5-Carboxylate Dehydrogenase. J.Mol.Biol. (2006)
- Release Date
- 2006-07-24
- Peptides
- 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
BE
AF
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.80 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x FLC: CITRATE ANION(Non-covalent)
- 24 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
- 15 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)
- 6 x NA: SODIUM ION(Non-functional Binders)
- 6 x CL: CHLORIDE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Inagaki, E. et al., Crystal Structure of Thermus Thermophilus Delta(1)- Pyrroline-5-Carboxylate Dehydrogenase. J.Mol.Biol. (2006)
- Release Date
- 2006-07-24
- Peptides
- 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
BE
AF
B