- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.65 Å
- Oligo State
- homo-hexamer
- Ligands
- 12 x ACT: ACETATE ION(Non-functional Binders)
- 6 x NA: SODIUM ION(Non-functional Binders)
NA.3: 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.13: 4 residues within 4Å:- Chain B: S.55, L.56, E.123, D.211
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:L.56, B:L.56
- Water bridges: B:D.211, B:D.211
NA.22: 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:S.55, C:L.56
NA.32: 4 residues within 4Å:- Chain D: S.55, L.56, E.123, D.211
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:L.56, D:L.56
- Water bridges: D:D.211, D:D.211
NA.41: 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:D.211
NA.51: 4 residues within 4Å:- Chain F: S.55, L.56, E.123, D.211
4 PLIP interactions:4 interactions with chain F- Hydrogen bonds: F:L.56, F:D.211
- Water bridges: F:D.211, F:D.211
- 6 x ALA: ALANINE(Non-covalent)
ALA.4: 7 residues within 4Å:- Chain A: F.185, C.322, S.323, T.476, G.477, A.478, F.485
10 PLIP interactions:8 interactions with chain A, 2 Ligand-Ligand interactions- Hydrophobic interactions: A:F.185, A:F.485
- Hydrogen bonds: A:S.323, A:G.477, A:A.478
- Water bridges: A:E.137, A:E.137, A:E.137, A.4, A.4
ALA.14: 7 residues within 4Å:- Chain B: F.185, C.322, S.323, T.476, G.477, A.478, F.485
10 PLIP interactions:9 interactions with chain B, 1 Ligand-Ligand interactions- Hydrophobic interactions: B:F.185, B:F.485
- Hydrogen bonds: B:S.323, B:G.477, B:A.478
- Water bridges: B:E.137, B:E.137, B:E.137, B:E.137, A.14
ALA.23: 7 residues within 4Å:- Chain C: F.185, C.322, S.323, T.476, G.477, A.478, F.485
10 PLIP interactions:8 interactions with chain C, 2 Ligand-Ligand interactions- Hydrophobic interactions: C:F.185, C:F.485
- Hydrogen bonds: C:S.323, C:G.477, C:A.478
- Water bridges: C:E.137, C:E.137, C:E.137, A.23, A.23
ALA.33: 7 residues within 4Å:- Chain D: F.185, C.322, S.323, T.476, G.477, A.478, F.485
10 PLIP interactions:9 interactions with chain D, 1 Ligand-Ligand interactions- Hydrophobic interactions: D:F.185, D:F.485
- Hydrogen bonds: D:S.323, D:G.477, D:A.478
- Water bridges: D:E.137, D:E.137, D:E.137, D:E.137, A.33
ALA.42: 7 residues within 4Å:- Chain E: F.185, C.322, S.323, T.476, G.477, A.478, F.485
10 PLIP interactions:8 interactions with chain E, 2 Ligand-Ligand interactions- Hydrophobic interactions: E:F.185, E:F.485
- Hydrogen bonds: E:S.323, E:G.477, E:A.478
- Water bridges: E:E.137, E:E.137, E:E.137, A.42, A.42
ALA.52: 7 residues within 4Å:- Chain F: F.185, C.322, S.323, T.476, G.477, A.478, F.485
10 PLIP interactions:1 Ligand-Ligand interactions, 9 interactions with chain F- Water bridges: A.52, F:E.137, F:E.137, F:E.137, F:E.137
- Hydrophobic interactions: F:F.185, F:F.485
- Hydrogen bonds: F:S.323, F:G.477, F:A.478
- 6 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)
NAD.5: 28 residues within 4Å:- Chain A: I.180, A.181, P.182, W.183, N.184, I.189, K.207, P.208, A.209, E.210, G.240, E.241, G.244, A.245, F.258, T.259, G.260, S.261, V.264, E.288, T.289, G.290, C.322, E.417, F.419, L.445, F.485
- Ligands: ACT.1
12 PLIP interactions:12 interactions with chain A- Hydrophobic interactions: A:I.189, A:T.259
- Hydrogen bonds: A:A.181, A:A.181, A:W.183, A:K.207, A:E.210, A:G.240, A:S.261, A:G.290, A:E.417
- Water bridges: A:L.262
NAD.15: 28 residues within 4Å:- Chain B: I.180, A.181, P.182, W.183, N.184, I.189, K.207, P.208, A.209, E.210, G.240, E.241, G.244, A.245, F.258, T.259, G.260, S.261, V.264, E.288, T.289, G.290, C.322, E.417, F.419, L.445, F.485
- Ligands: ACT.11
15 PLIP interactions:15 interactions with chain B- Hydrophobic interactions: B:I.189, B:T.259
- Hydrogen bonds: B:A.181, B:A.181, B:W.183, B:K.207, B:E.210, B:G.240, B:S.261, B:T.289, B:E.417
- Water bridges: B:E.241, B:E.288, B:G.290, B:E.417
NAD.24: 28 residues within 4Å:- Chain C: I.180, A.181, P.182, W.183, N.184, I.189, K.207, P.208, A.209, E.210, G.240, E.241, G.244, A.245, F.258, T.259, G.260, S.261, V.264, E.288, T.289, G.290, C.322, E.417, F.419, L.445, F.485
- Ligands: ACT.20
12 PLIP interactions:12 interactions with chain C- Hydrophobic interactions: C:I.189, C:T.259
- Hydrogen bonds: C:A.181, C:A.181, C:W.183, C:K.207, C:E.210, C:G.240, C:S.261, C:G.290, C:E.417
- Water bridges: C:L.262
NAD.34: 28 residues within 4Å:- Chain D: I.180, A.181, P.182, W.183, N.184, I.189, K.207, P.208, A.209, E.210, G.240, E.241, G.244, A.245, F.258, T.259, G.260, S.261, V.264, E.288, T.289, G.290, C.322, E.417, F.419, L.445, F.485
- Ligands: ACT.30
15 PLIP interactions:15 interactions with chain D- Hydrophobic interactions: D:I.189, D:T.259
- Hydrogen bonds: D:A.181, D:A.181, D:W.183, D:K.207, D:E.210, D:G.240, D:S.261, D:T.289, D:E.417
- Water bridges: D:E.241, D:E.288, D:G.290, D:E.417
NAD.43: 28 residues within 4Å:- Chain E: I.180, A.181, P.182, W.183, N.184, I.189, K.207, P.208, A.209, E.210, G.240, E.241, G.244, A.245, F.258, T.259, G.260, S.261, V.264, E.288, T.289, G.290, C.322, E.417, F.419, L.445, F.485
- Ligands: ACT.39
12 PLIP interactions:12 interactions with chain E- Hydrophobic interactions: E:I.189, E:T.259
- Hydrogen bonds: E:A.181, E:A.181, E:W.183, E:K.207, E:E.210, E:G.240, E:S.261, E:G.290, E:E.417
- Water bridges: E:L.262
NAD.53: 28 residues within 4Å:- Chain F: I.180, A.181, P.182, W.183, N.184, I.189, K.207, P.208, A.209, E.210, G.240, E.241, G.244, A.245, F.258, T.259, G.260, S.261, V.264, E.288, T.289, G.290, C.322, E.417, F.419, L.445, F.485
- Ligands: ACT.49
15 PLIP interactions:15 interactions with chain F- Hydrophobic interactions: F:I.189, F:T.259
- Hydrogen bonds: F:A.181, F:A.181, F:W.183, F:K.207, F:E.210, F:G.240, F:S.261, F:T.289, F:E.417
- Water bridges: F:E.241, F:E.288, F:G.290, F:E.417
- 27 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
MPD.6: 6 residues within 4Å:- Chain A: E.158
- Chain B: F.6, Y.144, R.147, A.148, L.500
Ligand excluded by PLIPMPD.7: 4 residues within 4Å:- Chain A: V.312, Y.315, G.316, D.359
Ligand excluded by PLIPMPD.8: 5 residues within 4Å:- Chain A: R.151, Y.152, Y.171, L.500
- Ligands: MPD.19
Ligand excluded by PLIPMPD.9: 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 PLIPMPD.10: 5 residues within 4Å:- Chain A: L.275, G.278, Q.279
- Chain B: P.442, L.490
Ligand excluded by PLIPMPD.16: 5 residues within 4Å:- Chain B: R.36, Y.38, P.39, W.46, E.221
Ligand excluded by PLIPMPD.17: 3 residues within 4Å:- Chain B: P.353, E.355, E.356
Ligand excluded by PLIPMPD.18: 5 residues within 4Å:- Chain A: P.442, L.490
- Chain B: L.275, G.278, Q.279
Ligand excluded by PLIPMPD.19: 6 residues within 4Å:- Chain B: R.151, Y.152, A.156, Y.171, L.500
- Ligands: MPD.8
Ligand excluded by PLIPMPD.25: 6 residues within 4Å:- Chain C: E.158
- Chain D: F.6, Y.144, R.147, A.148, L.500
Ligand excluded by PLIPMPD.26: 4 residues within 4Å:- Chain C: V.312, Y.315, G.316, D.359
Ligand excluded by PLIPMPD.27: 5 residues within 4Å:- Chain C: R.151, Y.152, Y.171, L.500
- Ligands: MPD.38
Ligand excluded by PLIPMPD.28: 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 PLIPMPD.29: 5 residues within 4Å:- Chain C: L.275, G.278, Q.279
- Chain D: P.442, L.490
Ligand excluded by PLIPMPD.35: 5 residues within 4Å:- Chain D: R.36, Y.38, P.39, W.46, E.221
Ligand excluded by PLIPMPD.36: 3 residues within 4Å:- Chain D: P.353, E.355, E.356
Ligand excluded by PLIPMPD.37: 5 residues within 4Å:- Chain C: P.442, L.490
- Chain D: L.275, G.278, Q.279
Ligand excluded by PLIPMPD.38: 6 residues within 4Å:- Chain D: R.151, Y.152, A.156, Y.171, L.500
- Ligands: MPD.27
Ligand excluded by PLIPMPD.44: 6 residues within 4Å:- Chain E: E.158
- Chain F: F.6, Y.144, R.147, A.148, L.500
Ligand excluded by PLIPMPD.45: 4 residues within 4Å:- Chain E: V.312, Y.315, G.316, D.359
Ligand excluded by PLIPMPD.46: 5 residues within 4Å:- Chain E: R.151, Y.152, Y.171, L.500
- Ligands: MPD.57
Ligand excluded by PLIPMPD.47: 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 PLIPMPD.48: 5 residues within 4Å:- Chain E: L.275, G.278, Q.279
- Chain F: P.442, L.490
Ligand excluded by PLIPMPD.54: 5 residues within 4Å:- Chain F: R.36, Y.38, P.39, W.46, E.221
Ligand excluded by PLIPMPD.55: 3 residues within 4Å:- Chain F: P.353, E.355, E.356
Ligand excluded by PLIPMPD.56: 5 residues within 4Å:- Chain E: P.442, L.490
- Chain F: L.275, G.278, Q.279
Ligand excluded by PLIPMPD.57: 6 residues within 4Å:- Chain F: R.151, Y.152, A.156, Y.171, L.500
- Ligands: MPD.46
Ligand excluded by PLIP- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Inagaki, E. et al., Crystal structure analysis of delta1-pyrroline-5-carboxylate dehydrogenase in ternary complex with inhibitor and NAD. To be Published
- Release Date
- 2007-09-18
- 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 1.65 Å
- Oligo State
- homo-hexamer
- Ligands
- 12 x ACT: ACETATE ION(Non-functional Binders)
- 6 x NA: SODIUM ION(Non-functional Binders)
- 6 x ALA: ALANINE(Non-covalent)
- 6 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)
- 27 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Inagaki, E. et al., Crystal structure analysis of delta1-pyrroline-5-carboxylate dehydrogenase in ternary complex with inhibitor and NAD. To be Published
- Release Date
- 2007-09-18
- Peptides
- 1-pyrroline-5-carboxylate dehydrogenase: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
BE
AF
B