SMTL ID : 6xxh.1

Crystal Structure of Human Deoxyhypusine Synthase in apo form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

homo-tetramer

Ligands

2 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.1: 5 residues within 4Å: Chain A: N.173, Y.176, C.177, E.180, M.244 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.180, A:E.180 BME.5: 5 residues within 4Å: Chain C: N.173, Y.176, C.177, E.180, M.244 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.180

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

MRD.2: 4 residues within 4Å: Chain B: R.38, G.39, V.40, N.41 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.38 Water bridges: B:V.40 MRD.6: 4 residues within 4Å: Chain D: R.38, G.39, V.40, N.41 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.38 Water bridges: D:V.40

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 4 residues within 4Å: Chain B: Y.147, I.163, P.172 Chain C: S.28 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:S.28 Hydrophobic interactions: B:I.163 ACT.7: 4 residues within 4Å: Chain A: S.28 Chain D: Y.147, I.163, P.172 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:S.28 Hydrophobic interactions: D:I.163

2 x OXM: OXAMIC ACID(Non-covalent)

OXM.4: 5 residues within 4Å: Chain B: S.28 Chain C: Y.147, I.163, L.170, P.172 No protein-ligand interaction detected (PLIP) OXM.8: 5 residues within 4Å: Chain A: Y.147, I.163, L.170, P.172 Chain D: S.28 No protein-ligand interaction detected (PLIP)

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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