- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.80 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)
- 15 x ACT: ACETATE ION(Non-functional Binders)
ACT.2: 7 residues within 4Å:- Chain A: A.245, V.248, E.249, K.267, I.268, A.271
- Ligands: NAD.1
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:E.249, A:A.271
ACT.3: 6 residues within 4Å:- Chain A: R.461, R.462, F.464, H.465
- Chain B: V.172, K.510
7 PLIP interactions:2 interactions with chain A, 5 interactions with chain B- Hydrogen bonds: A:F.464
- Salt bridges: A:H.465, B:K.510
- Hydrophobic interactions: B:V.172, B:K.510
- Water bridges: B:K.91, B:K.91
ACT.4: 3 residues within 4Å:- Chain A: R.20, W.128, N.357
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:N.357
- Salt bridges: A:R.20
ACT.15: 7 residues within 4Å:- Chain B: A.245, V.248, E.249, K.267, I.268, A.271
- Ligands: NAD.13
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:A.271
ACT.16: 6 residues within 4Å:- Chain A: V.172, K.510
- Chain B: R.461, R.462, F.464, H.465
4 PLIP interactions:3 interactions with chain A, 1 interactions with chain B- Hydrophobic interactions: A:V.172, A:K.510
- Salt bridges: A:K.510, B:H.465
ACT.21: 7 residues within 4Å:- Chain C: A.245, V.248, E.249, K.267, I.268, A.271
- Ligands: NAD.20
2 PLIP interactions:2 interactions with chain C- Hydrophobic interactions: C:E.249, C:A.271
ACT.22: 6 residues within 4Å:- Chain C: R.461, R.462, F.464, H.465
- Chain D: V.172, K.510
7 PLIP interactions:5 interactions with chain D, 2 interactions with chain C- Hydrophobic interactions: D:V.172, D:K.510
- Water bridges: D:K.91, D:K.91
- Salt bridges: D:K.510, C:H.465
- Hydrogen bonds: C:F.464
ACT.23: 3 residues within 4Å:- Chain C: R.20, W.128, N.357
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:N.357
- Salt bridges: C:R.20
ACT.34: 7 residues within 4Å:- Chain D: A.245, V.248, E.249, K.267, I.268, A.271
- Ligands: NAD.32
1 PLIP interactions:1 interactions with chain D- Hydrophobic interactions: D:A.271
ACT.35: 6 residues within 4Å:- Chain C: V.172, K.510
- Chain D: R.461, R.462, F.464, H.465
4 PLIP interactions:3 interactions with chain C, 1 interactions with chain D- Hydrophobic interactions: C:V.172, C:K.510
- Salt bridges: C:K.510, D:H.465
ACT.40: 7 residues within 4Å:- Chain E: A.245, V.248, E.249, K.267, I.268, A.271
- Ligands: NAD.39
2 PLIP interactions:2 interactions with chain E- Hydrophobic interactions: E:E.249, E:A.271
ACT.41: 6 residues within 4Å:- Chain E: R.461, R.462, F.464, H.465
- Chain F: V.172, K.510
7 PLIP interactions:2 interactions with chain E, 5 interactions with chain F- Hydrogen bonds: E:F.464
- Salt bridges: E:H.465, F:K.510
- Hydrophobic interactions: F:V.172, F:K.510
- Water bridges: F:K.91, F:K.91
ACT.42: 3 residues within 4Å:- Chain E: R.20, W.128, N.357
2 PLIP interactions:2 interactions with chain E- Hydrogen bonds: E:N.357
- Salt bridges: E:R.20
ACT.53: 7 residues within 4Å:- Chain F: A.245, V.248, E.249, K.267, I.268, A.271
- Ligands: NAD.51
1 PLIP interactions:1 interactions with chain F- Hydrophobic interactions: F:A.271
ACT.54: 6 residues within 4Å:- Chain E: V.172, K.510
- Chain F: R.461, R.462, F.464, H.465
4 PLIP interactions:3 interactions with chain E, 1 interactions with chain F- Hydrophobic interactions: E:V.172, E:K.510
- Salt bridges: E:K.510, F:H.465
- 18 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)
MRD.5: 5 residues within 4Å:- Chain A: L.275, G.278, Q.279
- Chain B: P.442, L.490
Ligand excluded by PLIPMRD.7: 4 residues within 4Å:- Chain A: V.312, Y.315, G.316, D.359
Ligand excluded by PLIPMRD.11: 4 residues within 4Å:- Chain B: R.151, Y.171, L.500
- Ligands: MPD.9
Ligand excluded by PLIPMRD.12: 7 residues within 4Å:- Chain A: F.6, Y.144, R.147, A.148, L.500
- Chain B: E.158, V.160
Ligand excluded by PLIPMRD.17: 3 residues within 4Å:- Chain B: P.353, E.355, E.356
Ligand excluded by PLIPMRD.19: 5 residues within 4Å:- Chain A: P.442
- Chain B: L.275, G.278, Q.279, T.280
Ligand excluded by PLIPMRD.24: 5 residues within 4Å:- Chain C: L.275, G.278, Q.279
- Chain D: P.442, L.490
Ligand excluded by PLIPMRD.26: 4 residues within 4Å:- Chain C: V.312, Y.315, G.316, D.359
Ligand excluded by PLIPMRD.30: 4 residues within 4Å:- Chain D: R.151, Y.171, L.500
- Ligands: MPD.28
Ligand excluded by PLIPMRD.31: 7 residues within 4Å:- Chain C: F.6, Y.144, R.147, A.148, L.500
- Chain D: E.158, V.160
Ligand excluded by PLIPMRD.36: 3 residues within 4Å:- Chain D: P.353, E.355, E.356
Ligand excluded by PLIPMRD.38: 5 residues within 4Å:- Chain C: P.442
- Chain D: L.275, G.278, Q.279, T.280
Ligand excluded by PLIPMRD.43: 5 residues within 4Å:- Chain E: L.275, G.278, Q.279
- Chain F: P.442, L.490
Ligand excluded by PLIPMRD.45: 4 residues within 4Å:- Chain E: V.312, Y.315, G.316, D.359
Ligand excluded by PLIPMRD.49: 4 residues within 4Å:- Chain F: R.151, Y.171, L.500
- Ligands: MPD.47
Ligand excluded by PLIPMRD.50: 7 residues within 4Å:- Chain E: F.6, Y.144, R.147, A.148, L.500
- Chain F: E.158, V.160
Ligand excluded by PLIPMRD.55: 3 residues within 4Å:- Chain F: P.353, E.355, E.356
Ligand excluded by PLIPMRD.57: 5 residues within 4Å:- Chain E: P.442
- Chain F: L.275, G.278, Q.279, T.280
Ligand excluded by PLIP- 12 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
MPD.6: 4 residues within 4Å:- Chain A: R.36, P.39, W.46, E.221
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:W.46, A:W.46
- Hydrogen bonds: A:R.36
MPD.8: 5 residues within 4Å:- Chain A: K.371, S.374, Y.375, I.378, R.412
5 PLIP interactions:5 interactions with chain A- Hydrophobic interactions: A:K.371, A:I.378
- Water bridges: A:R.370, A:S.374, A:S.374
MPD.9: 5 residues within 4Å:- Chain A: R.151, Y.152, Y.171, L.500
- Ligands: MRD.11
6 PLIP interactions:5 interactions with chain A, 1 interactions with chain B- Hydrophobic interactions: A:Y.171, A:L.500
- Hydrogen bonds: A:R.151
- Water bridges: A:R.151, A:Y.171, B:D.501
MPD.14: 6 residues within 4Å:- Chain A: E.158
- Chain B: F.6, Y.144, R.147, A.148, L.500
6 PLIP interactions:1 interactions with chain A, 5 interactions with chain B- Hydrogen bonds: A:E.158
- Hydrophobic interactions: B:F.6, B:Y.144, B:R.147, B:A.148, B:L.500
MPD.25: 4 residues within 4Å:- Chain C: R.36, P.39, W.46, E.221
3 PLIP interactions:3 interactions with chain C- Hydrophobic interactions: C:W.46, C:W.46
- Hydrogen bonds: C:R.36
MPD.27: 5 residues within 4Å:- Chain C: K.371, S.374, Y.375, I.378, R.412
5 PLIP interactions:5 interactions with chain C- Hydrophobic interactions: C:K.371, C:I.378
- Water bridges: C:R.370, C:S.374, C:S.374
MPD.28: 5 residues within 4Å:- Chain C: R.151, Y.152, Y.171, L.500
- Ligands: MRD.30
6 PLIP interactions:5 interactions with chain C, 1 interactions with chain D- Hydrophobic interactions: C:Y.171, C:L.500
- Hydrogen bonds: C:R.151
- Water bridges: C:R.151, C:Y.171, D:D.501
MPD.33: 6 residues within 4Å:- Chain C: E.158
- Chain D: F.6, Y.144, R.147, A.148, L.500
6 PLIP interactions:5 interactions with chain D, 1 interactions with chain C- Hydrophobic interactions: D:F.6, D:Y.144, D:R.147, D:A.148, D:L.500
- Hydrogen bonds: C:E.158
MPD.44: 4 residues within 4Å:- Chain E: R.36, P.39, W.46, E.221
3 PLIP interactions:3 interactions with chain E- Hydrophobic interactions: E:W.46, E:W.46
- Hydrogen bonds: E:R.36
MPD.46: 5 residues within 4Å:- Chain E: K.371, S.374, Y.375, I.378, R.412
5 PLIP interactions:5 interactions with chain E- Hydrophobic interactions: E:K.371, E:I.378
- Water bridges: E:R.370, E:S.374, E:S.374
MPD.47: 5 residues within 4Å:- Chain E: R.151, Y.152, Y.171, L.500
- Ligands: MRD.49
6 PLIP interactions:5 interactions with chain E, 1 interactions with chain F- Hydrophobic interactions: E:Y.171, E:L.500
- Hydrogen bonds: E:R.151
- Water bridges: E:R.151, E:Y.171, F:D.501
MPD.52: 6 residues within 4Å:- Chain E: E.158
- Chain F: F.6, Y.144, R.147, A.148, L.500
6 PLIP interactions:1 interactions with chain E, 5 interactions with chain F- Hydrogen bonds: E:E.158
- Hydrophobic interactions: F:F.6, F:Y.144, F:R.147, F:A.148, F:L.500
- 6 x NA: SODIUM ION(Non-functional Binders)
NA.10: 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
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:L.56, B:L.56
- Water bridges: B:D.211
NA.29: 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
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:L.56, D:D.211
- Water bridges: D:D.211
NA.48: 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
3 PLIP interactions:3 interactions with chain F- Hydrogen bonds: F:L.56, F:D.211
- Water bridges: F:D.211
- 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
- 2006-03-09
- 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 NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)
- 15 x ACT: ACETATE ION(Non-functional Binders)
- 18 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)
- 12 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
- 6 x NA: SODIUM 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
- 2006-03-09
- Peptides
- 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
BE
AF
B