- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.35 Å
- Oligo State
- homo-12-mer
- Ligands
- 12 x SPM: SPERMINE(Non-covalent)
- 8 x SP5: N-[3-({4-[(3-aminopropyl)amino]butyl}amino)propyl]acetamide(Non-covalent)
SP5.2: 14 residues within 4Å:- Chain A: Y.33, W.34, F.35, I.77, E.87, F.88, Q.89, I.90, L.124, H.125, Y.137, E.151, F.152
- Chain C: R.163
11 PLIP interactions:10 interactions with chain A, 1 interactions with chain C- Hydrophobic interactions: A:F.35, A:I.77, A:Q.89, A:L.124, A:F.152
- Hydrogen bonds: A:Q.89, A:I.90, A:H.125, A:E.151, C:R.163
- Water bridges: A:H.125
SP5.6: 14 residues within 4Å:- Chain B: Y.33, W.34, F.35, I.77, E.78, E.87, F.88, Q.89, I.90, L.124, H.125, Y.137
- Chain H: E.78, Y.123
13 PLIP interactions:10 interactions with chain B, 3 interactions with chain H- Hydrophobic interactions: B:F.35, B:I.77, B:Q.89, B:L.124
- Hydrogen bonds: B:Q.89, B:I.90, B:H.125, H:E.78, H:Y.123
- Water bridges: B:E.78, B:E.78, B:H.125, H:Y.123
SP5.12: 14 residues within 4Å:- Chain D: Y.33, W.34, F.35, I.77, E.87, F.88, Q.89, I.90, L.124, H.125, Y.137, E.151, F.152
- Chain F: R.163
11 PLIP interactions:10 interactions with chain D, 1 interactions with chain F- Hydrophobic interactions: D:F.35, D:I.77, D:Q.89, D:L.124, D:F.152
- Hydrogen bonds: D:Q.89, D:I.90, D:H.125, D:E.151, F:R.163
- Water bridges: D:H.125
SP5.16: 14 residues within 4Å:- Chain E: Y.33, W.34, F.35, I.77, E.78, E.87, F.88, Q.89, I.90, L.124, H.125, Y.137
- Chain K: E.78, Y.123
13 PLIP interactions:10 interactions with chain E, 3 interactions with chain K- Hydrophobic interactions: E:F.35, E:I.77, E:Q.89, E:L.124
- Hydrogen bonds: E:Q.89, E:I.90, E:H.125, K:E.78, K:Y.123
- Water bridges: E:E.78, E:E.78, E:H.125, K:Y.123
SP5.22: 14 residues within 4Å:- Chain G: Y.33, W.34, F.35, I.77, E.87, F.88, Q.89, I.90, L.124, H.125, Y.137, E.151, F.152
- Chain I: R.163
13 PLIP interactions:12 interactions with chain G, 1 interactions with chain I- Hydrophobic interactions: G:F.35, G:I.77, G:Q.89, G:L.124, G:F.152
- Hydrogen bonds: G:Q.89, G:I.90, G:H.125, G:E.151, G:E.151, I:R.163
- Water bridges: G:H.125, G:Y.137
SP5.26: 14 residues within 4Å:- Chain B: E.78, Y.123
- Chain H: Y.33, W.34, F.35, I.77, E.78, E.87, F.88, Q.89, I.90, L.124, H.125, Y.137
11 PLIP interactions:2 interactions with chain B, 9 interactions with chain H- Hydrogen bonds: B:Y.123, B:Y.123, H:Q.89, H:I.90, H:H.125
- Hydrophobic interactions: H:F.35, H:I.77, H:Q.89, H:L.124
- Water bridges: H:E.78, H:H.125
SP5.32: 14 residues within 4Å:- Chain J: Y.33, W.34, F.35, I.77, E.87, F.88, Q.89, I.90, L.124, H.125, Y.137, E.151, F.152
- Chain L: R.163
13 PLIP interactions:12 interactions with chain J, 1 interactions with chain L- Hydrophobic interactions: J:F.35, J:I.77, J:Q.89, J:L.124, J:F.152
- Hydrogen bonds: J:Q.89, J:I.90, J:H.125, J:E.151, J:E.151, L:R.163
- Water bridges: J:H.125, J:Y.137
SP5.36: 14 residues within 4Å:- Chain E: E.78, Y.123
- Chain K: Y.33, W.34, F.35, I.77, E.78, E.87, F.88, Q.89, I.90, L.124, H.125, Y.137
11 PLIP interactions:9 interactions with chain K, 2 interactions with chain E- Hydrophobic interactions: K:F.35, K:I.77, K:Q.89, K:L.124
- Hydrogen bonds: K:Q.89, K:I.90, K:H.125, E:Y.123, E:Y.123
- Water bridges: K:E.78, K:H.125
- 12 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)
MRD.3: 5 residues within 4Å:- Chain A: Y.33, I.90, I.91, I.92, Q.97
6 PLIP interactions:6 interactions with chain A- Hydrophobic interactions: A:Y.33, A:Y.33, A:I.92
- Hydrogen bonds: A:I.92, A:I.92, A:Q.97
MRD.7: 7 residues within 4Å:- Chain B: I.92, A.102, K.132, A.133, L.136, Y.137
- Ligands: MRD.8
5 PLIP interactions:5 interactions with chain B- Hydrophobic interactions: B:I.92, B:A.102, B:L.136, B:Y.137
- Water bridges: B:N.130
MRD.8: 8 residues within 4Å:- Chain B: I.30, Y.33, I.90, I.91, I.92, Q.97, K.132
- Ligands: MRD.7
6 PLIP interactions:6 interactions with chain B- Hydrophobic interactions: B:I.30, B:Y.33, B:Y.33, B:I.91
- Hydrogen bonds: B:I.92, B:Q.97
MRD.13: 5 residues within 4Å:- Chain D: Y.33, I.90, I.91, I.92, Q.97
6 PLIP interactions:6 interactions with chain D- Hydrophobic interactions: D:Y.33, D:Y.33, D:I.92
- Hydrogen bonds: D:I.92, D:I.92, D:Q.97
MRD.17: 7 residues within 4Å:- Chain E: I.92, A.102, K.132, A.133, L.136, Y.137
- Ligands: MRD.18
5 PLIP interactions:5 interactions with chain E- Hydrophobic interactions: E:I.92, E:A.102, E:L.136, E:Y.137
- Water bridges: E:N.130
MRD.18: 8 residues within 4Å:- Chain E: I.30, Y.33, I.90, I.91, I.92, Q.97, K.132
- Ligands: MRD.17
6 PLIP interactions:6 interactions with chain E- Hydrophobic interactions: E:I.30, E:Y.33, E:Y.33, E:I.91
- Hydrogen bonds: E:I.92, E:Q.97
MRD.23: 5 residues within 4Å:- Chain G: Y.33, I.90, I.91, I.92, Q.97
6 PLIP interactions:6 interactions with chain G- Hydrophobic interactions: G:Y.33, G:Y.33, G:I.92
- Hydrogen bonds: G:I.92, G:I.92, G:Q.97
MRD.27: 7 residues within 4Å:- Chain H: I.92, A.102, K.132, A.133, L.136, Y.137
- Ligands: MRD.28
5 PLIP interactions:5 interactions with chain H- Hydrophobic interactions: H:I.92, H:A.102, H:L.136, H:Y.137
- Water bridges: H:N.130
MRD.28: 8 residues within 4Å:- Chain H: I.30, Y.33, I.90, I.91, I.92, Q.97, K.132
- Ligands: MRD.27
6 PLIP interactions:6 interactions with chain H- Hydrophobic interactions: H:I.30, H:Y.33, H:Y.33, H:I.91
- Hydrogen bonds: H:I.92, H:Q.97
MRD.33: 5 residues within 4Å:- Chain J: Y.33, I.90, I.91, I.92, Q.97
6 PLIP interactions:6 interactions with chain J- Hydrophobic interactions: J:Y.33, J:Y.33, J:I.92
- Hydrogen bonds: J:I.92, J:I.92, J:Q.97
MRD.37: 7 residues within 4Å:- Chain K: I.92, A.102, K.132, A.133, L.136, Y.137
- Ligands: MRD.38
5 PLIP interactions:5 interactions with chain K- Hydrophobic interactions: K:I.92, K:A.102, K:L.136, K:Y.137
- Water bridges: K:N.130
MRD.38: 8 residues within 4Å:- Chain K: I.30, Y.33, I.90, I.91, I.92, Q.97, K.132
- Ligands: MRD.37
6 PLIP interactions:6 interactions with chain K- Hydrophobic interactions: K:I.30, K:Y.33, K:Y.33, K:I.91
- Hydrogen bonds: K:I.92, K:Q.97
- 4 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)
TRS.4: 6 residues within 4Å:- Chain A: N.56, R.59, I.79, N.80, Y.81
- Chain B: Y.81
6 PLIP interactions:2 interactions with chain B, 4 interactions with chain A- Hydrogen bonds: B:Y.81, A:R.59, A:R.59, A:I.79
- Water bridges: B:R.84, A:Y.81
TRS.14: 6 residues within 4Å:- Chain D: N.56, R.59, I.79, N.80, Y.81
- Chain E: Y.81
6 PLIP interactions:4 interactions with chain D, 2 interactions with chain E- Hydrogen bonds: D:R.59, D:R.59, D:I.79, E:Y.81
- Water bridges: D:Y.81, E:R.84
TRS.24: 6 residues within 4Å:- Chain G: N.56, R.59, I.79, N.80, Y.81
- Chain H: Y.81
6 PLIP interactions:4 interactions with chain G, 2 interactions with chain H- Hydrogen bonds: G:R.59, G:R.59, G:I.79, H:Y.81
- Water bridges: G:Y.81, H:R.84
TRS.34: 6 residues within 4Å:- Chain J: N.56, R.59, I.79, N.80, Y.81
- Chain K: Y.81
6 PLIP interactions:4 interactions with chain J, 2 interactions with chain K- Hydrogen bonds: J:R.59, J:R.59, J:I.79, K:Y.81
- Water bridges: J:Y.81, K:R.84
- 4 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
MPD.9: 3 residues within 4Å:- Chain B: E.47, K.51
- Chain G: H.54
1 PLIP interactions:1 interactions with chain B- Water bridges: B:K.51
MPD.19: 3 residues within 4Å:- Chain E: E.47, K.51
- Chain J: H.54
1 PLIP interactions:1 interactions with chain E- Water bridges: E:K.51
MPD.29: 3 residues within 4Å:- Chain A: H.54
- Chain H: E.47, K.51
1 PLIP interactions:1 interactions with chain H- Water bridges: H:K.51
MPD.39: 3 residues within 4Å:- Chain D: H.54
- Chain K: E.47, K.51
1 PLIP interactions:1 interactions with chain K- Water bridges: K:K.51
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Filippova, E.V. et al., Crystal structure of product-bound complex of spermidine/spermine N-acetyltransferase SpeG from Vibrio cholerae. To Be Published
- Release Date
- 2019-07-10
- Peptides
- Spermidine N(1)-acetyltransferase: ABCDEFGHIJKL
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
DC
ED
AE
DF
EG
AH
DI
EJ
AK
DL
E
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.35 Å
- Oligo State
- homo-12-mer
- Ligands
- 12 x SPM: SPERMINE(Non-covalent)
- 8 x SP5: N-[3-({4-[(3-aminopropyl)amino]butyl}amino)propyl]acetamide(Non-covalent)
- 12 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)
- 4 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)
- 4 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Filippova, E.V. et al., Crystal structure of product-bound complex of spermidine/spermine N-acetyltransferase SpeG from Vibrio cholerae. To Be Published
- Release Date
- 2019-07-10
- Peptides
- Spermidine N(1)-acetyltransferase: ABCDEFGHIJKL
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
DC
ED
AE
DF
EG
AH
DI
EJ
AK
DL
E