- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.80 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x NA: SODIUM ION(Non-functional Binders)
- 4 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.5
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
5 PLIP interactions:3 interactions with chain B, 2 interactions with chain A- Hydrophobic interactions: B:V.172, B:K.510
- Salt bridges: B:K.510, A:H.465
- Hydrogen bonds: A:F.464
ACT.12: 7 residues within 4Å:- Chain B: A.245, V.248, E.249, K.267, I.268, A.271
- Ligands: NAD.16
4 PLIP interactions:4 interactions with chain B- Hydrophobic interactions: B:V.248, B:A.271
- Water bridges: B:K.267, B:K.267
ACT.13: 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
- 2 x SER: SERINE(Non-covalent)
SER.4: 8 residues within 4Å:- Chain A: F.185, K.321, C.322, S.323, T.476, G.477, A.478, F.485
10 PLIP interactions:8 interactions with chain A, 2 Ligand-Ligand interactions- Hydrogen bonds: A:C.322, A:S.323, A:S.323, A:G.477, A:A.478, S.4, S.4
- Water bridges: A:E.137, A:E.137, A:A.478
SER.15: 7 residues within 4Å:- Chain B: F.185, C.322, S.323, T.476, G.477, A.478, F.485
9 PLIP interactions:8 interactions with chain B, 1 Ligand-Ligand interactions- Hydrogen bonds: B:C.322, B:S.323, B:S.323, B:G.477, B:A.478
- Water bridges: B:E.137, B:E.137, B:A.478, S.15
- 2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)
NAD.5: 29 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, I.268, E.288, T.289, G.290, C.322, E.417, F.419, L.445, F.485
- Ligands: ACT.2
17 PLIP interactions:17 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:E.241, A:S.261, A:T.289, A:E.417
- Water bridges: A:W.183, A:S.261, A:G.290, A:E.417, A:E.417
NAD.16: 29 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, I.268, E.288, T.289, G.290, C.322, E.417, F.419, L.445, F.485
- Ligands: ACT.12
18 PLIP interactions:18 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:S.261, B:K.267, B:K.267, B:E.288, B:E.288, B:G.290
- 13 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
MPD.6: 4 residues within 4Å:- Chain A: V.312, Y.315, G.316, D.359
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:V.312
- Water bridges: A:E.308, A:V.312
MPD.7: 6 residues within 4Å:- Chain A: F.6, Y.144, R.147, A.148, L.500
- Chain B: E.158
6 PLIP interactions:5 interactions with chain A, 1 interactions with chain B- Hydrophobic interactions: A:F.6, A:Y.144, A:R.147, A:A.148, A:L.500
- Water bridges: B:E.158
MPD.8: 3 residues within 4Å:- Chain A: Y.154, F.170
- Chain B: R.462
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:Y.154, A:F.170, A:F.170
- Water bridges: A:D.92
MPD.9: 5 residues within 4Å:- Chain A: R.36, Y.38, P.39, W.46, E.221
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:Y.38, A:W.46
- Hydrogen bonds: A:R.36
MPD.10: 6 residues within 4Å:- Chain A: L.275, G.278, Q.279, T.280
- Chain B: P.442, L.490
5 PLIP interactions:3 interactions with chain A, 2 interactions with chain B- Hydrophobic interactions: A:L.275, A:T.280, B:P.442, B:L.490
- Hydrogen bonds: A:G.278
MPD.11: 5 residues within 4Å:- Chain A: R.151, A.156, Y.171, L.500
- Ligands: MPD.17
7 PLIP interactions:2 interactions with chain B, 5 interactions with chain A- Water bridges: B:D.501, B:D.501, A:Y.171
- Hydrophobic interactions: A:R.151, A:A.156, A:Y.171, A:L.500
MPD.17: 6 residues within 4Å:- Chain B: R.151, Y.152, A.156, Y.171, L.500
- Ligands: MPD.11
7 PLIP interactions:5 interactions with chain B, 2 interactions with chain A- Hydrophobic interactions: B:R.151, B:A.156, B:Y.171, B:L.500
- Water bridges: B:Y.171, A:D.501, A:D.501
MPD.18: 6 residues within 4Å:- Chain A: E.158
- Chain B: F.6, Y.144, R.147, A.148, L.500
6 PLIP interactions:5 interactions with chain B, 1 interactions with chain A- Hydrophobic interactions: B:F.6, B:Y.144, B:R.147, B:A.148, B:L.500
- Hydrogen bonds: A:E.158
MPD.19: 3 residues within 4Å:- Chain A: R.462
- Chain B: Y.154, F.170
2 PLIP interactions:2 interactions with chain B- Hydrophobic interactions: B:Y.154
- Water bridges: B:D.92
MPD.20: 3 residues within 4Å:- Chain B: P.353, E.355, E.356
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:E.356
MPD.21: 5 residues within 4Å:- Chain A: P.442
- Chain B: L.275, G.278, Q.279, T.280
4 PLIP interactions:3 interactions with chain B, 1 interactions with chain A- Hydrophobic interactions: B:L.275, B:T.280, A:P.442
- Hydrogen bonds: B:G.278
MPD.22: 4 residues within 4Å:- Chain B: R.36, Y.38, W.46, E.221
8 PLIP interactions:8 interactions with chain B- Hydrophobic interactions: B:Y.38, B:W.46, B:W.46, B:W.46, B:E.221
- Hydrogen bonds: B:R.36, B:E.221, B:E.221
MPD.23: 4 residues within 4Å:- Chain B: V.312, Y.315, G.316, D.359
No protein-ligand interaction detected (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
- 2007-09-11
- Peptides
- 1-pyrroline-5-carboxylate dehydrogenase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.80 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x NA: SODIUM ION(Non-functional Binders)
- 4 x ACT: ACETATE ION(Non-functional Binders)
- 2 x SER: SERINE(Non-covalent)
- 2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)
- 13 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
- 2007-09-11
- Peptides
- 1-pyrroline-5-carboxylate dehydrogenase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B