SMTL ID : 6e1x.2 (1 other biounit)

Crystal structure of product-bound complex of spermidine/spermine N-acetyltransferase SpeG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-12-mer

Ligands

12 x SPM: SPERMINE(Non-covalent)

SPM.1: 13 residues within 4Å: Chain A: N.25, M.31, W.34, E.36, E.37, Y.39, E.40, E.44 Chain I: H.52, I.53, D.55, E.58, R.59 9 PLIP interactions: 2 interactions with chain I, 7 interactions with chain A Hydrogen bonds: I:I.53, I:D.55, A:E.37, A:E.44 Hydrophobic interactions: A:E.37 Water bridges: A:N.25, A:N.25, A:N.25, A:Y.39 SPM.5: 13 residues within 4Å: Chain A: H.52, I.53, D.55, E.58, R.59 Chain B: N.25, M.31, W.34, E.36, E.37, Y.39, E.40, E.44 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:E.37 Hydrogen bonds: B:E.36, B:E.36, B:E.37, B:E.44, A:I.53, A:D.55 Water bridges: B:N.25, B:N.25, B:Y.39 SPM.6: 9 residues within 4Å: Chain B: H.52, I.53, D.55, E.58, R.59 Chain J: Y.81 Chain L: E.37, E.40, E.44 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain L Hydrogen bonds: B:I.53, B:D.55, L:E.44 Water bridges: L:E.44, L:E.44 SPM.11: 13 residues within 4Å: Chain D: N.25, M.31, W.34, E.36, E.37, Y.39, E.40, E.44 Chain L: H.52, I.53, D.55, E.58, R.59 9 PLIP interactions: 2 interactions with chain L, 7 interactions with chain D Hydrogen bonds: L:I.53, L:D.55, D:E.37, D:E.44 Hydrophobic interactions: D:E.37 Water bridges: D:N.25, D:N.25, D:N.25, D:Y.39 SPM.15: 13 residues within 4Å: Chain D: H.52, I.53, D.55, E.58, R.59 Chain E: N.25, M.31, W.34, E.36, E.37, Y.39, E.40, E.44 10 PLIP interactions: 8 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:E.37 Hydrogen bonds: E:E.36, E:E.36, E:E.37, E:E.44, D:I.53, D:D.55 Water bridges: E:N.25, E:N.25, E:Y.39 SPM.16: 9 residues within 4Å: Chain E: H.52, I.53, D.55, E.58, R.59 Chain G: Y.81 Chain I: E.37, E.40, E.44 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain I Hydrogen bonds: E:I.53, E:D.55, I:E.44 Water bridges: I:E.44, I:E.44 SPM.21: 13 residues within 4Å: Chain C: H.52, I.53, D.55, E.58, R.59 Chain G: N.25, M.31, W.34, E.36, E.37, Y.39, E.40, E.44 11 PLIP interactions: 9 interactions with chain G, 2 interactions with chain C Hydrophobic interactions: G:E.37 Hydrogen bonds: G:E.37, G:E.44, C:I.53, C:D.55 Water bridges: G:N.25, G:N.25, G:N.25, G:Y.39, G:Y.39, G:E.44 SPM.25: 13 residues within 4Å: Chain G: H.52, I.53, D.55, E.58, R.59 Chain H: N.25, M.31, W.34, E.36, E.37, Y.39, E.40, E.44 11 PLIP interactions: 2 interactions with chain G, 9 interactions with chain H Hydrogen bonds: G:I.53, G:D.55, H:E.36, H:E.37, H:E.44 Hydrophobic interactions: H:E.37 Water bridges: H:N.25, H:N.25, H:Y.39, H:Y.39, H:E.44 SPM.26: 9 residues within 4Å: Chain D: Y.81 Chain F: E.37, E.40, E.44 Chain H: H.52, I.53, D.55, E.58, R.59 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain F Hydrogen bonds: H:I.53, H:D.55, F:E.44 Water bridges: F:E.44 SPM.31: 13 residues within 4Å: Chain F: H.52, I.53, D.55, E.58, R.59 Chain J: N.25, M.31, W.34, E.36, E.37, Y.39, E.40, E.44 11 PLIP interactions: 2 interactions with chain F, 9 interactions with chain J Hydrogen bonds: F:I.53, F:D.55, J:E.37, J:E.44 Hydrophobic interactions: J:E.37 Water bridges: J:N.25, J:N.25, J:N.25, J:Y.39, J:Y.39, J:E.44 SPM.35: 13 residues within 4Å: Chain J: H.52, I.53, D.55, E.58, R.59 Chain K: N.25, M.31, W.34, E.36, E.37, Y.39, E.40, E.44 11 PLIP interactions: 9 interactions with chain K, 2 interactions with chain J Hydrophobic interactions: K:E.37 Hydrogen bonds: K:E.36, K:E.37, K:E.44, J:I.53, J:D.55 Water bridges: K:N.25, K:N.25, K:Y.39, K:Y.39, K:E.44 SPM.36: 9 residues within 4Å: Chain A: Y.81 Chain C: E.37, E.40, E.44 Chain K: H.52, I.53, D.55, E.58, R.59 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain K Hydrogen bonds: C:E.44, K:I.53, K:D.55 Water bridges: C:E.44

4 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 SP5.12: 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 SP5.22: 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 SP5.32: 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

8 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 5 residues within 4Å: Chain A: Y.33, I.90, I.91, I.92, Q.97 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.33, A:Y.33 Hydrogen bonds: A:I.92, A:I.92, A:Q.97 MPD.10: 3 residues within 4Å: Chain A: H.54 Chain B: E.47, K.51 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:H.54, B:K.51 Hydrogen bonds: B:K.51 MPD.13: 5 residues within 4Å: Chain D: Y.33, I.90, I.91, I.92, Q.97 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:Y.33, D:Y.33 Hydrogen bonds: D:I.92, D:I.92, D:Q.97 MPD.20: 3 residues within 4Å: Chain D: H.54 Chain E: E.47, K.51 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:H.54, E:K.51 Hydrogen bonds: E:K.51 MPD.23: 5 residues within 4Å: Chain G: Y.33, I.90, I.91, I.92, Q.97 5 PLIP interactions: 5 interactions with chain G Hydrophobic interactions: G:Y.33, G:Y.33 Hydrogen bonds: G:I.92, G:I.92, G:Q.97 MPD.30: 3 residues within 4Å: Chain G: H.54 Chain H: E.47, K.51 3 PLIP interactions: 1 interactions with chain G, 2 interactions with chain H Hydrophobic interactions: G:H.54, H:K.51 Hydrogen bonds: H:K.51 MPD.33: 5 residues within 4Å: Chain J: Y.33, I.90, I.91, I.92, Q.97 5 PLIP interactions: 5 interactions with chain J Hydrophobic interactions: J:Y.33, J:Y.33 Hydrogen bonds: J:I.92, J:I.92, J:Q.97 MPD.40: 3 residues within 4Å: Chain J: H.54 Chain K: E.47, K.51 3 PLIP interactions: 1 interactions with chain J, 2 interactions with chain K Hydrophobic interactions: J:H.54, K:K.51 Hydrogen bonds: K:K.51

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 K: Y.81 6 PLIP interactions: 1 interactions with chain K, 5 interactions with chain A Hydrogen bonds: K:Y.81, A:N.56, A:R.59, A:R.59 Water bridges: A:I.79, A:Y.81 TRS.14: 6 residues within 4Å: Chain D: N.56, R.59, I.79, N.80, Y.81 Chain H: Y.81 6 PLIP interactions: 1 interactions with chain H, 5 interactions with chain D Hydrogen bonds: H:Y.81, D:N.56, D:R.59, D:R.59 Water bridges: D:I.79, D:Y.81 TRS.24: 6 residues within 4Å: Chain E: Y.81 Chain G: N.56, R.59, I.79, N.80, Y.81 6 PLIP interactions: 5 interactions with chain G, 1 interactions with chain E Hydrogen bonds: G:N.56, G:R.59, G:R.59, E:Y.81 Water bridges: G:I.79, G:Y.81 TRS.34: 6 residues within 4Å: Chain B: Y.81 Chain J: N.56, R.59, I.79, N.80, Y.81 6 PLIP interactions: 5 interactions with chain J, 1 interactions with chain B Hydrogen bonds: J:N.56, J:R.59, J:R.59, B:Y.81 Water bridges: J:I.79, J:Y.81

4 x HLG: N-{3-[(4-aminobutyl)amino]propyl}acetamide(Non-covalent)

HLG.7: 11 residues within 4Å: Chain B: Y.33, W.34, F.35, I.77, E.87, F.88, Q.89, I.90, L.124, H.125, Y.137 10 PLIP interactions: 10 interactions with chain B 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 Water bridges: B:E.87, B:E.87, B:H.125 HLG.17: 11 residues within 4Å: Chain E: Y.33, W.34, F.35, I.77, E.87, F.88, Q.89, I.90, L.124, H.125, Y.137 10 PLIP interactions: 10 interactions with chain E 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 Water bridges: E:E.87, E:E.87, E:H.125 HLG.27: 11 residues within 4Å: Chain H: Y.33, W.34, F.35, I.77, E.87, F.88, Q.89, I.90, L.124, H.125, Y.137 12 PLIP interactions: 11 interactions with chain H, 1 interactions with chain E Hydrophobic interactions: H:F.35, H:I.77, H:Q.89, H:L.124 Hydrogen bonds: H:Q.89, H:I.90, H:H.125 Water bridges: H:E.87, H:E.87, H:H.125, H:Y.137, E:E.78 HLG.37: 11 residues within 4Å: Chain K: Y.33, W.34, F.35, I.77, E.87, F.88, Q.89, I.90, L.124, H.125, Y.137 12 PLIP interactions: 11 interactions with chain K, 1 interactions with chain B 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 Water bridges: K:E.87, K:E.87, K:H.125, K:Y.137, B:E.78

8 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.8: 7 residues within 4Å: Chain B: I.92, A.102, K.132, A.133, L.136, Y.137 Ligands: MRD.9 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.92, B:A.102, B:A.133, B:L.136, B:Y.137 Water bridges: B:N.130, B:Y.137 MRD.9: 8 residues within 4Å: Chain B: I.30, Y.33, I.90, I.91, I.92, Q.97, K.132 Ligands: MRD.8 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.30, B:Y.33, B:Y.33 Hydrogen bonds: B:I.92, B:Q.97 MRD.18: 7 residues within 4Å: Chain E: I.92, A.102, K.132, A.133, L.136, Y.137 Ligands: MRD.19 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:I.92, E:A.102, E:A.133, E:L.136, E:Y.137 Water bridges: E:N.130, E:Y.137 MRD.19: 8 residues within 4Å: Chain E: I.30, Y.33, I.90, I.91, I.92, Q.97, K.132 Ligands: MRD.18 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:I.30, E:Y.33, E:Y.33 Hydrogen bonds: E:I.92, E:Q.97 MRD.28: 7 residues within 4Å: Chain H: I.92, A.102, K.132, A.133, L.136, Y.137 Ligands: MRD.29 7 PLIP interactions: 7 interactions with chain H Hydrophobic interactions: H:I.92, H:A.102, H:A.133, H:L.136, H:Y.137 Water bridges: H:Y.137, H:Y.137 MRD.29: 8 residues within 4Å: Chain H: I.30, Y.33, I.90, I.91, I.92, Q.97, K.132 Ligands: MRD.28 5 PLIP interactions: 5 interactions with chain H Hydrophobic interactions: H:I.30, H:Y.33, H:Y.33 Hydrogen bonds: H:I.92, H:Q.97 MRD.38: 7 residues within 4Å: Chain K: I.92, A.102, K.132, A.133, L.136, Y.137 Ligands: MRD.39 7 PLIP interactions: 7 interactions with chain K Hydrophobic interactions: K:I.92, K:A.102, K:A.133, K:L.136, K:Y.137 Water bridges: K:Y.137, K:Y.137 MRD.39: 8 residues within 4Å: Chain K: I.30, Y.33, I.90, I.91, I.92, Q.97, K.132 Ligands: MRD.38 5 PLIP interactions: 5 interactions with chain K Hydrophobic interactions: K:I.30, K:Y.33, K:Y.33 Hydrogen bonds: K:I.92, K:Q.97

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
B

B
C

C
F

D
B

E
C

F
F

G
B

H
C

I
F

J
B

K
C

L
F

Spermidine N(1)-acetyltransferase

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