SMTL ID : 8a0e.1

CryoEM structure of DHS-eIF5A1 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-1-mer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 25 residues within 4Å: Chain A: T.106, S.107, N.108, L.109, T.133, A.134, G.135, E.138, I.168, D.240, G.284, G.285, N.309, T.310, A.311, D.344, A.345 Chain B: G.286, V.287, H.290, D.315, S.317, D.318, S.319 Ligands: SPD.4 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.107, A:S.107, A:N.108, A:T.133, A:A.134, A:G.135, A:G.285, A:N.309, A:T.310, A:D.344, A:A.345, B:D.318, B:S.319, B:S.319 NAD.3: 25 residues within 4Å: Chain A: G.286, V.287, H.290, D.315, S.317, D.318, S.319 Chain B: T.106, S.107, N.108, L.109, T.133, A.134, G.135, I.168, D.240, G.284, G.285, I.308, N.309, T.310, S.319, A.343, D.344, A.345 16 PLIP interactions: 11 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:S.107, B:N.108, B:A.134, B:G.135, B:D.240, B:G.285, B:T.310, B:T.310, B:S.319, B:S.319, B:A.345, A:D.315, A:D.318, A:S.319, A:S.319 pi-Stacking: A:H.290 NAD.5: 26 residues within 4Å: Chain C: T.106, S.107, N.108, L.109, T.133, A.134, G.135, E.138, I.168, D.240, G.284, G.285, N.309, T.310, A.311, A.343, D.344, A.345 Chain D: G.286, V.287, H.290, D.315, S.317, D.318, S.319 Ligands: SPD.2 15 PLIP interactions: 12 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:S.107, C:S.107, C:N.108, C:T.133, C:T.133, C:A.134, C:G.135, C:G.285, C:T.310, C:D.344, C:D.344, C:A.345, D:D.318, D:S.319, D:S.319 NAD.7: 25 residues within 4Å: Chain C: G.286, V.287, H.290, D.315, S.317, D.318, S.319 Chain D: T.106, S.107, N.108, L.109, T.133, A.134, G.135, I.168, D.240, G.284, G.285, N.309, T.310, A.311, S.319, D.344, A.345 Ligands: SPD.6 19 PLIP interactions: 15 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:T.106, D:S.107, D:S.107, D:N.108, D:T.133, D:T.133, D:A.134, D:G.135, D:G.285, D:T.310, D:S.319, D:S.319, D:D.344, D:D.344, D:A.345, C:D.315, C:D.318, C:S.319, C:S.319

3 x SPD: SPERMIDINE(Non-covalent)

SPD.2: 6 residues within 4Å: Chain A: V.19 Chain C: Y.178 Chain D: H.290, D.318, W.329 Ligands: NAD.5 5 PLIP interactions: 1 interactions with chain A, 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: A:V.19, D:D.318, D:D.318 Hydrophobic interactions: D:W.329, C:Y.178 SPD.4: 8 residues within 4Å: Chain A: I.168, D.245 Chain B: H.290, N.294, D.318, E.325, W.329 Ligands: NAD.1 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:D.318 Hydrogen bonds: B:N.294, B:E.325, A:D.245 SPD.6: 8 residues within 4Å: Chain C: H.290, D.318, E.325, W.329 Chain D: G.241, S.242, D.245 Ligands: NAD.7 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:W.329 Hydrogen bonds: C:E.325, D:D.245

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

2023-04-05

Peptides

Deoxyhypusine synthase: ABCD
Eukaryotic translation initiation factor 5A: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Deoxyhypusine synthase

Eukaryotic translation initiation factor 5A

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