SMTL ID : 6d72.1

Crystal structure of spermidine/spermine N-acetyltransferase SpeG from Yersinia pestis in complex with calcium ions.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

homo-12-mer

Ligands

12 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: E.38, E.79 Chain B: E.38, E.79 Ligands: CA.2 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:E.38, A:E.79, B:E.38, H2O.1, H2O.4 CA.2: 4 residues within 4Å: Chain A: E.38 Chain B: E.38, E.79 Ligands: CA.1 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:E.38, B:E.38, B:E.79, H2O.3, H2O.5 CA.7: 4 residues within 4Å: Chain C: E.38 Chain I: E.38, E.79 Ligands: CA.31 5 PLIP interactions: 2 interactions with chain I, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: I:E.38, I:E.79, C:E.38, H2O.7, H2O.21 CA.13: 5 residues within 4Å: Chain D: E.38, E.79 Chain E: E.38, E.79 Ligands: CA.14 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: D:E.38, D:E.79, E:E.38, H2O.8, H2O.12 CA.14: 4 residues within 4Å: Chain D: E.38 Chain E: E.38, E.79 Ligands: CA.13 5 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: E:E.38, E:E.79, D:E.38, H2O.11, H2O.12 CA.19: 4 residues within 4Å: Chain F: E.38 Chain L: E.38, E.79 Ligands: CA.43 5 PLIP interactions: 2 interactions with chain L, 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: L:E.38, L:E.79, F:E.38, H2O.14, H2O.28 CA.25: 5 residues within 4Å: Chain G: E.38, E.79 Chain H: E.38, E.79 Ligands: CA.26 5 PLIP interactions: 1 interactions with chain H, 2 interactions with chain G, 2 Ligand-Water interactions Metal complexes: H:E.38, G:E.38, G:E.79, H2O.16, H2O.19 CA.26: 4 residues within 4Å: Chain G: E.38 Chain H: E.38, E.79 Ligands: CA.25 5 PLIP interactions: 2 interactions with chain H, 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: H:E.38, H:E.79, G:E.38, H2O.18, H2O.19 CA.31: 4 residues within 4Å: Chain C: E.38, E.79 Chain I: E.38 Ligands: CA.7 5 PLIP interactions: 1 interactions with chain I, 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: I:E.38, C:E.38, C:E.79, H2O.7, H2O.22 CA.37: 5 residues within 4Å: Chain J: E.38, E.79 Chain K: E.38, E.79 Ligands: CA.38 5 PLIP interactions: 2 interactions with chain J, 1 interactions with chain K, 2 Ligand-Water interactions Metal complexes: J:E.38, J:E.79, K:E.38, H2O.23, H2O.26 CA.38: 4 residues within 4Å: Chain J: E.38 Chain K: E.38, E.79 Ligands: CA.37 5 PLIP interactions: 2 interactions with chain K, 1 interactions with chain J, 2 Ligand-Water interactions Metal complexes: K:E.38, K:E.79, J:E.38, H2O.25, H2O.26 CA.43: 4 residues within 4Å: Chain F: E.38, E.79 Chain L: E.38 Ligands: CA.19 5 PLIP interactions: 2 interactions with chain F, 1 interactions with chain L, 2 Ligand-Water interactions Metal complexes: F:E.38, F:E.79, L:E.38, H2O.14, H2O.29

8 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 5 residues within 4Å: Chain A: Y.35, F.37, E.38, E.60 Chain B: N.81 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.38, B:N.81 Water bridges: B:R.86 PEG.5: 3 residues within 4Å: Chain B: P.21, F.44 Chain D: E.16 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.16 PEG.15: 5 residues within 4Å: Chain D: Y.35, F.37, E.38, E.60 Chain E: N.81 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:E.38, E:N.81 Water bridges: E:R.86 PEG.17: 3 residues within 4Å: Chain A: E.16 Chain E: P.21, F.44 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.16 PEG.27: 5 residues within 4Å: Chain G: Y.35, F.37, E.38, E.60 Chain H: N.81 3 PLIP interactions: 1 interactions with chain G, 2 interactions with chain H Hydrogen bonds: G:E.38, H:N.81 Water bridges: H:R.86 PEG.29: 3 residues within 4Å: Chain H: P.21, F.44 Chain J: E.16 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:E.16 PEG.39: 5 residues within 4Å: Chain J: Y.35, F.37, E.38, E.60 Chain K: N.81 3 PLIP interactions: 2 interactions with chain K, 1 interactions with chain J Hydrogen bonds: K:N.81, J:E.38 Water bridges: K:R.86 PEG.41: 3 residues within 4Å: Chain G: E.16 Chain K: P.21, F.44 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:E.16

28 x MLI: MALONATE ION(Non-functional Binders)

MLI.4: 5 residues within 4Å: Chain A: E.79, E.152, F.153 Chain B: Y.124 Ligands: MLI.6 Ligand excluded by PLIP MLI.6: 4 residues within 4Å: Chain B: E.79, E.152, F.153 Ligands: MLI.4 Ligand excluded by PLIP MLI.8: 7 residues within 4Å: Chain C: I.126, E.152 Chain I: R.86, Y.124, R.164 Ligands: MLI.9, MLI.33 Ligand excluded by PLIP MLI.9: 7 residues within 4Å: Chain C: R.86 Chain I: E.79, E.152, F.153 Ligands: MLI.8, MLI.32, MLI.33 Ligand excluded by PLIP MLI.10: 6 residues within 4Å: Chain C: R.34, Y.35, Y.41, L.74, E.76, I.92 Ligand excluded by PLIP MLI.11: 4 residues within 4Å: Chain C: P.21, H.24, N.28, F.44 Ligand excluded by PLIP MLI.12: 3 residues within 4Å: Chain C: I.126, F.153, I.155 Ligand excluded by PLIP MLI.16: 5 residues within 4Å: Chain D: E.79, E.152, F.153 Chain E: Y.124 Ligands: MLI.18 Ligand excluded by PLIP MLI.18: 4 residues within 4Å: Chain E: E.79, E.152, F.153 Ligands: MLI.16 Ligand excluded by PLIP MLI.20: 7 residues within 4Å: Chain F: I.126, E.152 Chain L: R.86, Y.124, R.164 Ligands: MLI.21, MLI.45 Ligand excluded by PLIP MLI.21: 7 residues within 4Å: Chain F: R.86 Chain L: E.79, E.152, F.153 Ligands: MLI.20, MLI.44, MLI.45 Ligand excluded by PLIP MLI.22: 6 residues within 4Å: Chain F: R.34, Y.35, Y.41, L.74, E.76, I.92 Ligand excluded by PLIP MLI.23: 4 residues within 4Å: Chain F: P.21, H.24, N.28, F.44 Ligand excluded by PLIP MLI.24: 3 residues within 4Å: Chain F: I.126, F.153, I.155 Ligand excluded by PLIP MLI.28: 5 residues within 4Å: Chain G: E.79, E.152, F.153 Chain H: Y.124 Ligands: MLI.30 Ligand excluded by PLIP MLI.30: 4 residues within 4Å: Chain H: E.79, E.152, F.153 Ligands: MLI.28 Ligand excluded by PLIP MLI.32: 7 residues within 4Å: Chain C: R.86, Y.124, R.164 Chain I: I.126, E.152 Ligands: MLI.9, MLI.33 Ligand excluded by PLIP MLI.33: 7 residues within 4Å: Chain C: E.79, E.152, F.153 Chain I: R.86 Ligands: MLI.8, MLI.9, MLI.32 Ligand excluded by PLIP MLI.34: 6 residues within 4Å: Chain I: R.34, Y.35, Y.41, L.74, E.76, I.92 Ligand excluded by PLIP MLI.35: 4 residues within 4Å: Chain I: P.21, H.24, N.28, F.44 Ligand excluded by PLIP MLI.36: 3 residues within 4Å: Chain I: I.126, F.153, I.155 Ligand excluded by PLIP MLI.40: 5 residues within 4Å: Chain J: E.79, E.152, F.153 Chain K: Y.124 Ligands: MLI.42 Ligand excluded by PLIP MLI.42: 4 residues within 4Å: Chain K: E.79, E.152, F.153 Ligands: MLI.40 Ligand excluded by PLIP MLI.44: 7 residues within 4Å: Chain F: R.86, Y.124, R.164 Chain L: I.126, E.152 Ligands: MLI.21, MLI.45 Ligand excluded by PLIP MLI.45: 7 residues within 4Å: Chain F: E.79, E.152, F.153 Chain L: R.86 Ligands: MLI.20, MLI.21, MLI.44 Ligand excluded by PLIP MLI.46: 6 residues within 4Å: Chain L: R.34, Y.35, Y.41, L.74, E.76, I.92 Ligand excluded by PLIP MLI.47: 4 residues within 4Å: Chain L: P.21, H.24, N.28, F.44 Ligand excluded by PLIP MLI.48: 3 residues within 4Å: Chain L: I.126, F.153, I.155 Ligand excluded by PLIP

Links

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Citation

Filippova, E.V. et al., Crystal structure of spermidine/spermine N-acetyltransferase SpeG from Yersinia pestis in complex with calcium ions. To Be Published

Release Date

2018-05-16

Peptides

Spermidine N1-acetyltransferase: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

G
A

H
B

I
C

J
A

K
B

L
C

Spermidine N1-acetyltransferase