SMTL ID : 6cx8.1

Crystal structure of spermidine/spermine N-acetyltransferase SpeG from Vibrio cholerae in complex with manganese ions.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

homo-12-mer

Ligands

6 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: E.36, E.78 Chain B: E.36, E.78 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Metal complexes: A:E.36, A:E.36, A:E.78, B:E.36, B:E.78 MN.5: 4 residues within 4Å: Chain C: E.36, E.78 Chain D: E.36, E.78 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Metal complexes: C:E.36, C:E.78, D:E.36, D:E.78, D:E.78 MN.9: 4 residues within 4Å: Chain E: E.36, E.78 Chain F: E.36, E.78 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain F Metal complexes: E:E.36, E:E.78, F:E.36, F:E.78, F:E.78 MN.12: 4 residues within 4Å: Chain G: E.36, E.78 Chain H: E.36, E.78 5 PLIP interactions: 2 interactions with chain H, 3 interactions with chain G Metal complexes: H:E.36, H:E.78, G:E.36, G:E.36, G:E.78 MN.16: 4 residues within 4Å: Chain I: E.36, E.78 Chain J: E.36, E.78 5 PLIP interactions: 3 interactions with chain J, 2 interactions with chain I Metal complexes: J:E.36, J:E.78, J:E.78, I:E.36, I:E.78 MN.20: 4 residues within 4Å: Chain K: E.36, E.78 Chain L: E.36, E.78 5 PLIP interactions: 3 interactions with chain L, 2 interactions with chain K Metal complexes: L:E.36, L:E.78, L:E.78, K:E.36, K:E.78

6 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.2: 2 residues within 4Å: Chain A: H.125, I.154 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.154 Water bridges: A:A.127 IPA.4: 5 residues within 4Å: Chain B: N.25, N.29, I.30, E.40 Chain C: Y.112 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.112 Water bridges: C:A.12 IPA.6: 3 residues within 4Å: Chain C: N.25, N.29, E.40 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.25, C:N.25, C:N.29 IPA.13: 2 residues within 4Å: Chain G: H.125, I.154 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:I.154 Water bridges: G:A.127 IPA.15: 5 residues within 4Å: Chain H: N.25, N.29, I.30, E.40 Chain I: Y.112 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:Y.112 Water bridges: I:A.12 IPA.17: 3 residues within 4Å: Chain I: N.25, N.29, E.40 3 PLIP interactions: 3 interactions with chain I Hydrogen bonds: I:N.25, I:N.25, I:N.29

8 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 6 residues within 4Å: Chain A: I.92, G.98, K.99, G.100, F.101, A.102 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.98, A:G.100, A:G.100, A:F.101, A:A.102 PO4.7: 6 residues within 4Å: Chain C: Q.97, G.98, K.99, G.100, F.101, A.102 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.98, C:G.98, C:G.100, C:A.102 PO4.8: 7 residues within 4Å: Chain D: I.92, Q.97, G.98, K.99, G.100, F.101, A.102 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:G.98, D:G.100, D:G.100, D:F.101, D:A.102 Water bridges: D:K.99, D:K.99, D:R.103 PO4.10: 5 residues within 4Å: Chain E: G.98, K.99, G.100, F.101, A.102 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:G.98, E:G.98, E:G.100, E:A.102 PO4.14: 6 residues within 4Å: Chain G: I.92, G.98, K.99, G.100, F.101, A.102 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:G.98, G:G.100, G:G.100, G:F.101, G:A.102 PO4.18: 6 residues within 4Å: Chain I: Q.97, G.98, K.99, G.100, F.101, A.102 4 PLIP interactions: 4 interactions with chain I Hydrogen bonds: I:G.98, I:G.98, I:G.100, I:A.102 PO4.19: 7 residues within 4Å: Chain J: I.92, Q.97, G.98, K.99, G.100, F.101, A.102 8 PLIP interactions: 8 interactions with chain J Hydrogen bonds: J:G.98, J:G.100, J:G.100, J:F.101, J:A.102 Water bridges: J:K.99, J:K.99, J:R.103 PO4.21: 5 residues within 4Å: Chain K: G.98, K.99, G.100, F.101, A.102 4 PLIP interactions: 4 interactions with chain K Hydrogen bonds: K:G.98, K:G.98, K:G.100, K:A.102

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

MPD.11: 4 residues within 4Å: Chain F: H.125, V.126, A.127, N.130 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:A.127 MPD.22: 4 residues within 4Å: Chain L: H.125, V.126, A.127, N.130 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:A.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2018-04-18

Peptides

Spermidine N(1)-acetyltransferase: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
A

H
B

I
C

J
D

K
E

L
F

Spermidine N(1)-acetyltransferase

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