- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.10 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x PRO: PROLINE(Non-covalent)
- 6 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)
NAD.2: 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.3
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:S.261, A:S.261, A:T.289, A:E.417
- Water bridges: A:W.183, A:E.241, A:E.241, A:E.241, A:G.290
NAD.9: 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.10
17 PLIP interactions:17 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:S.261, B:K.267, B:E.288, B:G.290
NAD.18: 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.19
17 PLIP interactions:17 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:S.261, C:T.289, C:E.417
- Water bridges: C:W.183, C:E.241, C:E.241, C:E.241, C:G.290
NAD.25: 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.26
17 PLIP interactions:17 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:S.261, D:S.261, D:K.267, D:E.288, D:G.290
NAD.34: 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.35
17 PLIP interactions:17 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:S.261, E:T.289, E:E.417
- Water bridges: E:W.183, E:E.241, E:E.241, E:E.241, E:G.290
NAD.41: 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.42
17 PLIP interactions:17 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:S.261, F:S.261, F:K.267, F:E.288, F:G.290
- 12 x ACT: ACETATE ION(Non-functional Binders)
ACT.3: 7 residues within 4Å:- Chain A: A.245, V.248, E.249, K.267, I.268, A.271
- Ligands: NAD.2
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:E.249, A:A.271
ACT.4: 6 residues within 4Å:- Chain A: R.461, R.462, F.464, H.465
- Chain B: V.172, K.510
4 PLIP interactions:3 interactions with chain B, 1 interactions with chain A- Hydrophobic interactions: B:V.172, B:K.510
- Salt bridges: B:K.510, A:H.465
ACT.10: 7 residues within 4Å:- Chain B: A.245, V.248, E.249, K.267, I.268, A.271
- Ligands: NAD.9
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:A.271
ACT.11: 6 residues within 4Å:- Chain A: V.172, K.510
- Chain B: R.461, R.462, F.464, H.465
6 PLIP interactions:2 interactions with chain B, 4 interactions with chain A- Hydrogen bonds: B:F.464
- Salt bridges: B:H.465, A:K.510
- Hydrophobic interactions: A:V.172, A:K.510
- Water bridges: A:K.91
ACT.19: 7 residues within 4Å:- Chain C: A.245, V.248, E.249, K.267, I.268, A.271
- Ligands: NAD.18
2 PLIP interactions:2 interactions with chain C- Hydrophobic interactions: C:E.249, C:A.271
ACT.20: 6 residues within 4Å:- Chain C: R.461, R.462, F.464, H.465
- Chain D: V.172, K.510
4 PLIP interactions:3 interactions with chain D, 1 interactions with chain C- Hydrophobic interactions: D:V.172, D:K.510
- Salt bridges: D:K.510, C:H.465
ACT.26: 7 residues within 4Å:- Chain D: A.245, V.248, E.249, K.267, I.268, A.271
- Ligands: NAD.25
1 PLIP interactions:1 interactions with chain D- Hydrophobic interactions: D:A.271
ACT.27: 6 residues within 4Å:- Chain C: V.172, K.510
- Chain D: R.461, R.462, F.464, H.465
6 PLIP interactions:2 interactions with chain D, 4 interactions with chain C- Hydrogen bonds: D:F.464
- Salt bridges: D:H.465, C:K.510
- Hydrophobic interactions: C:V.172, C:K.510
- Water bridges: C:K.91
ACT.35: 7 residues within 4Å:- Chain E: A.245, V.248, E.249, K.267, I.268, A.271
- Ligands: NAD.34
2 PLIP interactions:2 interactions with chain E- Hydrophobic interactions: E:E.249, E:A.271
ACT.36: 6 residues within 4Å:- Chain E: R.461, R.462, F.464, H.465
- Chain F: V.172, K.510
4 PLIP interactions:1 interactions with chain E, 3 interactions with chain F- Salt bridges: E:H.465, F:K.510
- Hydrophobic interactions: F:V.172, F:K.510
ACT.42: 7 residues within 4Å:- Chain F: A.245, V.248, E.249, K.267, I.268, A.271
- Ligands: NAD.41
1 PLIP interactions:1 interactions with chain F- Hydrophobic interactions: F:A.271
ACT.43: 6 residues within 4Å:- Chain E: V.172, K.510
- Chain F: R.461, R.462, F.464, H.465
6 PLIP interactions:2 interactions with chain F, 4 interactions with chain E- Hydrogen bonds: F:F.464
- Salt bridges: F:H.465, E:K.510
- Hydrophobic interactions: E:V.172, E:K.510
- Water bridges: E:K.91
- 6 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)
MRD.5: 4 residues within 4Å:- Chain A: V.312, Y.315, G.316, D.359
1 PLIP interactions:1 interactions with chain A- Hydrophobic interactions: A:V.312
MRD.15: 6 residues within 4Å:- Chain A: P.442, L.490
- Chain B: L.275, G.278, Q.279, T.280
6 PLIP interactions:2 interactions with chain A, 4 interactions with chain B- Hydrophobic interactions: A:P.442, A:L.490, B:L.275, B:T.280
- Hydrogen bonds: B:G.278, B:Q.279
MRD.21: 4 residues within 4Å:- Chain C: V.312, Y.315, G.316, D.359
1 PLIP interactions:1 interactions with chain C- Hydrophobic interactions: C:V.312
MRD.31: 6 residues within 4Å:- Chain C: P.442, L.490
- Chain D: L.275, G.278, Q.279, T.280
6 PLIP interactions:2 interactions with chain C, 4 interactions with chain D- Hydrophobic interactions: C:P.442, C:L.490, D:L.275, D:T.280
- Hydrogen bonds: D:G.278, D:Q.279
MRD.37: 4 residues within 4Å:- Chain E: V.312, Y.315, G.316, D.359
1 PLIP interactions:1 interactions with chain E- Hydrophobic interactions: E:V.312
MRD.47: 6 residues within 4Å:- Chain E: P.442, L.490
- Chain F: L.275, G.278, Q.279, T.280
6 PLIP interactions:2 interactions with chain E, 4 interactions with chain F- Hydrophobic interactions: E:P.442, E:L.490, F:L.275, F:T.280
- Hydrogen bonds: F:G.278, F:Q.279
- 6 x NA: SODIUM ION(Non-functional Binders)
NA.6: 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:L.56
NA.16: 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.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
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:L.56, D:E.123
- Water bridges: D:D.211
NA.38: 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.48: 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
- 12 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
MPD.8: 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.12: 6 residues within 4Å:- Chain A: F.6, Y.144, R.147, A.148, L.500
- Chain B: E.158
7 PLIP interactions:5 interactions with chain A, 2 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, B:V.160
MPD.13: 5 residues within 4Å:- Chain B: R.36, Y.38, P.39, W.46, E.221
8 PLIP interactions:8 interactions with chain B- Hydrophobic interactions: B:Y.38, B:P.39, B:W.46, B:W.46
- Hydrogen bonds: B:R.36, B:E.221
- Water bridges: B:W.46, B:E.221
MPD.14: 3 residues within 4Å:- Chain B: P.353, E.355, E.356
No protein-ligand interaction detected (PLIP)MPD.24: 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.28: 6 residues within 4Å:- Chain C: F.6, Y.144, R.147, A.148, L.500
- Chain D: E.158
7 PLIP interactions:2 interactions with chain D, 5 interactions with chain C- Water bridges: D:E.158, D:V.160
- Hydrophobic interactions: C:F.6, C:Y.144, C:R.147, C:A.148, C:L.500
MPD.29: 5 residues within 4Å:- Chain D: R.36, Y.38, P.39, W.46, E.221
8 PLIP interactions:8 interactions with chain D- Hydrophobic interactions: D:Y.38, D:P.39, D:W.46, D:W.46
- Hydrogen bonds: D:R.36, D:E.221
- Water bridges: D:W.46, D:E.221
MPD.30: 3 residues within 4Å:- Chain D: P.353, E.355, E.356
No protein-ligand interaction detected (PLIP)MPD.40: 6 residues within 4Å:- Chain E: E.158
- Chain F: F.6, Y.144, R.147, A.148, L.500
6 PLIP interactions:5 interactions with chain F, 1 interactions with chain E- Hydrophobic interactions: F:F.6, F:Y.144, F:R.147, F:A.148, F:L.500
- Hydrogen bonds: E:E.158
MPD.44: 6 residues within 4Å:- Chain E: F.6, Y.144, R.147, A.148, L.500
- Chain F: E.158
7 PLIP interactions:5 interactions with chain E, 2 interactions with chain F- Hydrophobic interactions: E:F.6, E:Y.144, E:R.147, E:A.148, E:L.500
- Water bridges: F:E.158, F:V.160
MPD.45: 5 residues within 4Å:- Chain F: R.36, Y.38, P.39, W.46, E.221
8 PLIP interactions:8 interactions with chain F- Hydrophobic interactions: F:Y.38, F:P.39, F:W.46, F:W.46
- Hydrogen bonds: F:R.36, F:E.221
- Water bridges: F:W.46, F:E.221
MPD.46: 3 residues within 4Å:- Chain F: P.353, E.355, E.356
No protein-ligand interaction detected (PLIP)- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Inagaki, E. et al., Crystal Structure of Ternary Complex of Delta1-Pyrroline-5-Carboxylate Dehydrogenase with Substrate Mimic and Co-Factoer. To be Published
- Release Date
- 2007-10-02
- 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 2.10 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x PRO: PROLINE(Non-covalent)
- 6 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)
- 12 x ACT: ACETATE ION(Non-functional Binders)
- 6 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)
- 6 x NA: SODIUM ION(Non-functional Binders)
- 12 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 of Ternary Complex of Delta1-Pyrroline-5-Carboxylate Dehydrogenase with Substrate Mimic and Co-Factoer. To be Published
- Release Date
- 2007-10-02
- Peptides
- 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
BE
AF
B