SMTL ID : 6xxm.1

Crystal Structure of Human Deoxyhypusine Synthase in complex with putrescine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

homo-tetramer

Ligands

4 x PUT: 1,4-DIAMINOBUTANE(Non-covalent)

PUT.1: 12 residues within 4Å: Chain A: G.133, E.136, E.137, Y.176, G.239, S.240, D.243 Chain B: H.288, N.292, L.295, W.327, K.329 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.136, A:E.137, A:E.137, A:D.243, B:N.292 Hydrophobic interactions: B:W.327 PUT.3: 13 residues within 4Å: Chain A: H.288, N.292, L.295, W.327, K.329 Chain B: G.133, E.136, E.137, Y.176, G.239, S.240, D.243 Chain C: V.17 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.136, B:E.137, B:Y.176, B:D.243, A:N.292 Hydrophobic interactions: A:W.327 PUT.4: 12 residues within 4Å: Chain C: G.133, E.136, E.137, Y.176, G.239, S.240, D.243 Chain D: H.288, N.292, L.295, W.327, K.329 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:W.327 Hydrogen bonds: D:N.292, C:E.137, C:D.243 Water bridges: C:D.243 PUT.6: 13 residues within 4Å: Chain A: V.17 Chain C: H.288, N.292, L.295, W.327, K.329 Chain D: G.133, E.136, E.137, Y.176, G.239, S.240, D.243 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:E.137, D:E.137, D:Y.176, D:D.243, C:N.292 Hydrophobic interactions: C:W.327

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

MPD.2: 4 residues within 4Å: Chain B: R.38, G.39, V.40, N.41 2 PLIP interactions: 2 interactions with chain B Water bridges: B:N.37, B:V.40 MPD.5: 4 residues within 4Å: Chain D: R.38, G.39, V.40, N.41 2 PLIP interactions: 2 interactions with chain D Water bridges: D:N.37, D:V.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wator, E. et al., Half Way to Hypusine-Structural Basis for Substrate Recognition by Human Deoxyhypusine Synthase. Biomolecules (2020)

Release Date

2020-04-15

Peptides

Deoxyhypusine synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Deoxyhypusine synthase

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