SMTL ID : 7a6s.1

Crystal Structure of Asn173Ser variant of Human Deoxyhypusine Synthase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-tetramer

Ligands

14 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 8 residues within 4Å: Chain A: R.32, G.33, Y.34, D.35, R.38, A.44, A.48, T.51 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.38, A:T.51 Water bridges: A:G.33 EDO.4: 4 residues within 4Å: Chain A: S.28, T.29, Q.30, R.32 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.30 EDO.5: 6 residues within 4Å: Chain B: A.208, A.224, Q.225, H.228, I.229, P.230 1 PLIP interactions: 1 interactions with chain B Water bridges: B:A.208 EDO.6: 5 residues within 4Å: Chain B: R.43, Q.357 Chain C: V.40, Y.42 Ligands: EDO.9 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:R.43, B:R.43, B:Q.357, C:Y.42 EDO.7: 7 residues within 4Å: Chain A: S.105, I.166 Chain B: H.288, D.316, E.323, W.327, K.329 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:W.327 Water bridges: B:D.316, B:D.316, B:E.323, B:K.329, A:G.167 EDO.9: 5 residues within 4Å: Chain B: A.356, Q.357 Chain C: G.39, V.40 Ligands: EDO.6 No protein-ligand interaction detected (PLIP) EDO.10: 3 residues within 4Å: Chain B: S.28, T.29, Q.30 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.30 EDO.11: 8 residues within 4Å: Chain C: R.32, G.33, Y.34, D.35, R.38, A.44, A.48, T.51 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.38, C:T.51 Water bridges: C:G.33 EDO.14: 4 residues within 4Å: Chain C: S.28, T.29, Q.30, R.32 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.30 EDO.15: 6 residues within 4Å: Chain D: A.208, A.224, Q.225, H.228, I.229, P.230 1 PLIP interactions: 1 interactions with chain D Water bridges: D:A.208 EDO.16: 5 residues within 4Å: Chain A: V.40, Y.42 Chain D: R.43, Q.357 Ligands: EDO.19 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:Y.42, D:R.43, D:R.43, D:Q.357 EDO.17: 7 residues within 4Å: Chain C: S.105, I.166 Chain D: H.288, D.316, E.323, W.327, K.329 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:D.316, D:E.323, D:W.327 Water bridges: D:D.316, D:D.316, D:E.323, D:K.329, C:G.167 EDO.19: 5 residues within 4Å: Chain A: G.39, V.40 Chain D: A.356, Q.357 Ligands: EDO.16 No protein-ligand interaction detected (PLIP) EDO.20: 3 residues within 4Å: Chain D: S.28, T.29, Q.30 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.30

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

ACT.2: 4 residues within 4Å: Chain A: Y.147, I.163, L.170, P.172 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.147 ACT.3: 5 residues within 4Å: Chain A: S.28 Chain D: Y.147, I.163, L.170, P.172 No protein-ligand interaction detected (PLIP) ACT.12: 4 residues within 4Å: Chain C: Y.147, I.163, L.170, P.172 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.147 ACT.13: 5 residues within 4Å: Chain B: Y.147, I.163, L.170, P.172 Chain C: S.28 No protein-ligand interaction detected (PLIP)

2 x OXM: OXAMIC ACID(Non-covalent)

OXM.8: 3 residues within 4Å: Chain B: R.38, G.39, V.40 2 PLIP interactions: 2 interactions with chain B Water bridges: B:V.40, B:V.40 OXM.18: 3 residues within 4Å: Chain D: R.38, G.39, V.40 2 PLIP interactions: 2 interactions with chain D Water bridges: D:V.40, D:V.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wator, E. et al., Cryo-EM structure of human eIF5A-DHS complex reveals the molecular basis of hypusination-associated neurodegenerative disorders. Nat Commun (2023)

Release Date

2022-03-23

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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