SMTL ID : 8a0g.1

Human deoxyhypusine synthase with trapped transition state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-tetramer

Ligands

2 x 13D: 1,3-DIAMINOPROPANE(Non-covalent)

13D.1: 10 residues within 4Å: Chain A: H.290, N.294, L.297, W.329, K.331 Chain B: E.138, G.241, S.242, D.245 Ligands: NAD.5 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.138, B:Y.178, B:Y.178, B:S.242, B:D.245, A:N.294 13D.6: 10 residues within 4Å: Chain C: H.290, N.294, L.297, W.329, K.331 Chain D: E.138, G.241, S.242, D.245 Ligands: NAD.10 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:Y.178, D:S.242, D:D.245, C:N.294 Water bridges: D:D.245

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

MRD.2: 3 residues within 4Å: Chain A: R.40, G.41, V.42 1 PLIP interactions: 1 interactions with chain A Water bridges: A:V.42 MRD.7: 3 residues within 4Å: Chain C: R.40, G.41, V.42 1 PLIP interactions: 1 interactions with chain C Water bridges: C:V.42

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

NAD.3: 31 residues within 4Å: Chain A: T.106, S.107, N.108, L.109, S.111, T.133, A.134, G.135, E.138, E.139, I.168, D.240, G.284, G.285, I.308, N.309, T.310, A.311, A.343, D.344, A.345 Chain B: G.286, V.287, H.290, D.315, S.317, D.318, S.319, K.331 Ligands: SPD.4, NAD.5 25 PLIP interactions: 17 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:S.107, A:S.107, A:N.108, A:S.111, A:T.133, A:A.134, A:G.135, A:E.139, A:D.240, A:G.285, A:T.310, A:T.310, A:D.344, A:A.345, B:G.286, B:D.318, B:S.319, B:S.319, B:S.319, B:S.319 Water bridges: A:N.108, A:N.108, A:G.285, B:V.287, B:S.317 NAD.5: 30 residues within 4Å: Chain A: G.286, V.287, H.290, D.315, S.317, D.318, S.319, K.331 Chain B: T.106, S.107, N.108, L.109, S.111, T.133, A.134, G.135, E.138, E.139, D.240, G.284, G.285, I.308, N.309, T.310, A.311, A.343, D.344, A.345 Ligands: 13D.1, NAD.3 24 PLIP interactions: 17 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:S.107, B:S.107, B:N.108, B:S.111, B:T.133, B:A.134, B:G.135, B:E.139, B:D.240, B:G.285, B:T.310, B:D.344, B:A.345, A:D.318, A:S.319, A:S.319, A:S.319 Water bridges: B:N.108, B:N.108, B:G.285, B:T.310, A:V.287, A:D.318, A:D.318 NAD.8: 31 residues within 4Å: Chain C: T.106, S.107, N.108, L.109, S.111, T.133, A.134, G.135, E.138, E.139, I.168, D.240, G.284, G.285, I.308, 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, K.331 Ligands: SPD.9, NAD.10 27 PLIP interactions: 19 interactions with chain C, 8 interactions with chain D Hydrogen bonds: C:T.106, C:S.107, C:S.107, C:N.108, C:S.111, C:T.133, C:T.133, C:A.134, C:G.135, C:E.139, C:G.285, C:T.310, C:D.344, C:D.344, C:A.345, D:G.286, D:D.318, D:S.319, D:S.319, D:S.319, D:S.319 Water bridges: C:N.108, C:N.108, C:G.285, C:T.310, D:V.287, D:D.318 NAD.10: 30 residues within 4Å: Chain C: G.286, V.287, H.290, D.315, S.317, D.318, S.319, K.331 Chain D: T.106, S.107, N.108, L.109, S.111, T.133, A.134, G.135, E.138, E.139, D.240, G.284, G.285, I.308, N.309, T.310, A.311, A.343, D.344, A.345 Ligands: 13D.6, NAD.8 27 PLIP interactions: 19 interactions with chain D, 8 interactions with chain C Hydrogen bonds: D:T.106, D:S.107, D:S.107, D:N.108, D:S.111, D:T.133, D:T.133, D:A.134, D:G.135, D:E.139, D:G.285, D:T.310, D:T.310, D:D.344, D:D.344, D:A.345, C:D.318, C:S.319, C:S.319, C:S.319 Water bridges: D:N.108, D:N.108, D:G.285, C:V.287, C:S.317, C:D.318, C:D.318

2 x SPD: SPERMIDINE(Non-covalent)

SPD.4: 11 residues within 4Å: Chain A: G.241, S.242, D.245 Chain B: H.290, N.294, L.297, D.318, E.325, W.329, K.331 Ligands: NAD.3 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.329, B:W.329 Hydrogen bonds: B:N.294, B:D.318, B:E.325, A:D.245 SPD.9: 11 residues within 4Å: Chain C: G.241, S.242, D.245 Chain D: H.290, N.294, L.297, D.318, E.325, W.329, K.331 Ligands: NAD.8 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:W.329, D:W.329 Hydrogen bonds: D:N.294, D:E.325, C:D.245 Water bridges: D:E.325

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Deoxyhypusine synthase