SMTL ID : 8a0f.1

Crystal structure of human deoxyhypusine synthase variant K329A in complex with NAD and SPD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

homo-tetramer

Ligands

4 x SPD: SPERMIDINE(Non-covalent)

SPD.1: 11 residues within 4Å: Chain A: H.290, N.294, L.297, D.318, E.325, W.329 Chain B: I.168, G.241, S.242, D.245 Ligands: NAD.6 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.329, A:W.329 Hydrogen bonds: A:H.290, A:N.294, A:D.318, A:D.318, B:D.245 SPD.4: 11 residues within 4Å: Chain A: I.168, G.241, S.242, D.245 Chain B: H.290, N.294, L.297, D.318, E.325, W.329 Ligands: NAD.3 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:D.245, B:H.290, B:N.294, B:D.318 Hydrophobic interactions: B:W.329, B:W.329 SPD.7: 11 residues within 4Å: Chain C: H.290, N.294, L.297, D.318, E.325, W.329 Chain D: I.168, G.241, S.242, D.245 Ligands: NAD.12 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:W.329, C:W.329 Hydrogen bonds: C:H.290, C:N.294, C:D.318, D:D.245 Water bridges: C:E.325 SPD.10: 11 residues within 4Å: Chain C: I.168, G.241, S.242, D.245 Chain D: H.290, N.294, L.297, D.318, E.325, W.329 Ligands: NAD.9 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:W.329, D:W.329 Hydrogen bonds: D:H.290, D:N.294, D:D.318, D:D.318, C:D.245 Water bridges: D:E.325

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

EDO.2: 6 residues within 4Å: Chain A: L.89, Q.91, E.263, R.266, L.267, T.270 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.89, A:E.263, A:R.266 EDO.8: 6 residues within 4Å: Chain C: L.89, Q.91, E.263, R.266, L.267, T.270 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:L.89, C:E.263, C:R.266

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

NAD.3: 30 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 Ligands: SPD.4, NAD.6 24 PLIP interactions: 9 interactions with chain B, 15 interactions with chain A Hydrogen bonds: B:G.286, B:D.318, B:S.319, B:S.319, B:S.319, B:S.319, 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:D.344, A:A.345 Water bridges: B:V.287, B:S.317, B:D.318, A:N.108, A:N.108 NAD.6: 30 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, 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 Ligands: SPD.1, NAD.3 25 PLIP interactions: 8 interactions with chain A, 17 interactions with chain B Hydrogen bonds: A:G.286, A:D.318, A:S.319, A:S.319, A:S.319, A:S.319, 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:T.310, B:D.344, B:A.345 Water bridges: A:V.287, A:S.317, B:N.108, B:N.108, B:G.285 NAD.9: 30 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 Ligands: SPD.10, NAD.12 26 PLIP interactions: 18 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: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, D:V.287, D:S.317 NAD.12: 30 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, 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 Ligands: SPD.7, NAD.9 27 PLIP interactions: 9 interactions with chain C, 18 interactions with chain D Hydrogen bonds: C:G.286, C:D.318, C:S.319, C:S.319, C:S.319, C:S.319, 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:D.344, D:D.344, D:A.345 Water bridges: C:V.287, C:S.317, C:D.318, D:N.108, D:N.108, D:G.285

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

MRD.5: 3 residues within 4Å: Chain B: R.40, G.41, V.42 1 PLIP interactions: 1 interactions with chain B Water bridges: B:V.42 MRD.11: 3 residues within 4Å: Chain D: R.40, G.41, V.42 1 PLIP interactions: 1 interactions with chain D Water bridges: D:V.42

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

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