SMTL ID : 7a6t.1

Crystal Structure of Asn173Ser variant of Human Deoxyhypusine Synthase in complex with NAD and spermidine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 38 residues within 4Å: Chain A: T.104, S.105, N.106, L.107, S.109, T.131, A.132, G.133, E.136, E.137, I.166, D.238, G.239, S.240, G.282, G.283, G.284, I.306, N.307, T.308, A.309, S.317, A.341, D.342, A.343, S.344 Chain B: G.284, V.285, H.288, A.309, D.313, G.314, S.315, D.316, S.317 Chain D: F.54 Ligands: NAD.9, SPD.10 23 PLIP interactions: 9 interactions with chain B, 14 interactions with chain A Hydrogen bonds: B:G.284, B:D.316, B:S.317, B:S.317, B:S.317, B:S.317, A:S.105, A:N.106, A:T.131, A:A.132, A:G.133, A:D.238, A:D.238, A:G.282, A:G.283, A:T.308, A:D.342, A:A.343 Water bridges: B:V.285, B:G.314, B:D.316, A:N.106, A:V.285 NAD.9: 39 residues within 4Å: Chain A: G.284, V.285, H.288, A.309, D.313, S.315, D.316, S.317 Chain B: T.104, S.105, N.106, L.107, S.109, T.131, A.132, G.133, E.136, E.137, I.166, A.235, D.238, G.239, S.240, G.282, G.283, G.284, V.285, I.306, N.307, T.308, A.309, S.317, A.341, D.342, A.343, S.344 Chain C: F.54 Ligands: NAD.1, SPD.2 21 PLIP interactions: 6 interactions with chain A, 15 interactions with chain B Hydrogen bonds: A:G.284, A:D.316, A:S.317, A:S.317, A:S.317, B:S.105, B:N.106, B:T.131, B:A.132, B:G.133, B:E.137, B:D.238, B:D.238, B:G.282, B:G.283, B:T.308, B:D.342, B:A.343 Water bridges: A:V.285, B:N.106, B:T.308 NAD.13: 38 residues within 4Å: Chain B: F.54 Chain C: T.104, S.105, N.106, L.107, S.109, T.131, A.132, G.133, E.136, E.137, I.166, D.238, G.239, S.240, G.282, G.283, G.284, I.306, N.307, T.308, A.309, S.317, A.341, D.342, A.343, S.344 Chain D: G.284, V.285, H.288, A.309, D.313, G.314, S.315, D.316, S.317 Ligands: NAD.21, SPD.22 22 PLIP interactions: 8 interactions with chain D, 14 interactions with chain C Hydrogen bonds: D:G.284, D:D.316, D:S.317, D:S.317, D:S.317, D:S.317, C:S.105, C:N.106, C:T.131, C:A.132, C:G.133, C:D.238, C:G.282, C:G.283, C:T.308, C:D.342, C:D.342, C:A.343 Water bridges: D:V.285, D:G.314, C:N.106, C:V.285 NAD.21: 39 residues within 4Å: Chain A: F.54 Chain C: G.284, V.285, H.288, A.309, D.313, S.315, D.316, S.317 Chain D: T.104, S.105, N.106, L.107, S.109, T.131, A.132, G.133, E.136, E.137, I.166, A.235, D.238, G.239, S.240, G.282, G.283, G.284, V.285, I.306, N.307, T.308, A.309, S.317, A.341, D.342, A.343, S.344 Ligands: NAD.13, SPD.14 22 PLIP interactions: 15 interactions with chain D, 7 interactions with chain C Hydrogen bonds: D:S.105, D:N.106, D:T.131, D:A.132, D:G.133, D:E.137, D:D.238, D:G.282, D:G.283, D:T.308, D:D.342, D:D.342, D:A.343, C:G.284, C:D.316, C:S.317, C:S.317, C:S.317 Water bridges: D:N.106, D:T.308, C:V.285, C:D.316

4 x SPD: SPERMIDINE(Non-covalent)

SPD.2: 19 residues within 4Å: Chain A: H.288, N.292, L.295, S.315, D.316, A.319, E.323, W.327, K.329 Chain B: E.136, R.165, I.166, G.167, Y.176, G.239, S.240, D.243 Ligands: EDO.3, NAD.9 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.327 Hydrogen bonds: A:N.292, A:D.316, A:E.323, A:K.329, B:D.243 Water bridges: B:D.243 SPD.10: 18 residues within 4Å: Chain A: R.165, I.166, G.167, Y.176, G.239, S.240, D.243 Chain B: H.288, N.292, L.295, D.316, A.319, E.323, W.327, K.329 Ligands: NAD.1, EDO.8, EDO.12 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.327 Hydrogen bonds: B:N.292, B:E.323, B:K.329, A:D.243 Water bridges: A:E.136, A:E.137 SPD.14: 19 residues within 4Å: Chain C: H.288, N.292, L.295, S.315, D.316, A.319, E.323, W.327, K.329 Chain D: E.136, R.165, I.166, G.167, Y.176, G.239, S.240, D.243 Ligands: EDO.15, NAD.21 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:D.243, C:N.292, C:E.323, C:K.329 Hydrophobic interactions: C:W.327 SPD.22: 18 residues within 4Å: Chain C: R.165, I.166, G.167, Y.176, G.239, S.240, D.243 Chain D: H.288, N.292, L.295, D.316, A.319, E.323, W.327, K.329 Ligands: NAD.13, EDO.20, EDO.24 9 PLIP interactions: 4 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:D.243, D:N.292, D:D.316, D:E.323, D:K.329 Water bridges: C:E.136, C:E.137, C:D.243 Hydrophobic interactions: D:W.327

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

EDO.3: 9 residues within 4Å: Chain A: K.287, H.288, A.291, Y.305, D.316, A.319, A.324, K.329 Ligands: SPD.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.287, A:D.316, A:K.329 Water bridges: A:H.288 EDO.4: 7 residues within 4Å: Chain A: R.32, G.33, Y.34, D.35, R.38, A.48, T.51 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.38 Water bridges: A:G.33 EDO.5: 6 residues within 4Å: Chain A: R.320, P.321, D.322, P.336 Chain B: R.154 Chain D: S.152 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: B:R.154, B:R.154, A:R.320, A:D.322, D:S.152 EDO.7: 3 residues within 4Å: Chain A: V.199, W.201, K.205 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.205 EDO.8: 8 residues within 4Å: Chain A: N.164, S.173, Y.176, S.240, M.244 Chain B: L.295, W.327 Ligands: SPD.10 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:W.327, A:S.173 EDO.12: 9 residues within 4Å: Chain B: K.287, H.288, A.291, Y.305, D.316, A.319, A.324, K.329 Ligands: SPD.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.287, B:K.329 Water bridges: B:Y.305 EDO.15: 9 residues within 4Å: Chain C: K.287, H.288, A.291, Y.305, D.316, A.319, A.324, K.329 Ligands: SPD.14 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.287, C:D.316, C:K.329 Water bridges: C:D.316, C:E.323 EDO.16: 7 residues within 4Å: Chain C: R.32, G.33, Y.34, D.35, R.38, A.48, T.51 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.38 Water bridges: C:G.33 EDO.17: 6 residues within 4Å: Chain B: S.152 Chain C: R.320, P.321, D.322, P.336 Chain D: R.154 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: B:S.152, C:R.320, C:D.322, D:R.154, D:R.154 EDO.19: 3 residues within 4Å: Chain C: V.199, W.201, K.205 1 PLIP interactions: 1 interactions with chain C Water bridges: C:K.205 EDO.20: 8 residues within 4Å: Chain C: N.164, S.173, Y.176, S.240, M.244 Chain D: L.295, W.327 Ligands: SPD.22 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Water bridges: D:W.327, C:S.173, C:D.243, C:D.243 EDO.24: 9 residues within 4Å: Chain D: K.287, H.288, A.291, Y.305, D.316, A.319, A.324, K.329 Ligands: SPD.22 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:K.287, D:E.323, D:K.329 Water bridges: D:Y.305

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

BME.6: 8 residues within 4Å: Chain A: L.87, T.88, Q.89, E.261, R.264, L.265, T.268 Chain B: Y.250 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.264 BME.18: 8 residues within 4Å: Chain C: L.87, T.88, Q.89, E.261, R.264, L.265, T.268 Chain D: Y.250 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.264

2 x OXM: OXAMIC ACID(Non-covalent)

OXM.11: 3 residues within 4Å: Chain B: R.38, G.39, V.40 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.38 Water bridges: B:V.40, B:V.40 OXM.23: 3 residues within 4Å: Chain D: R.38, G.39, V.40 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.38 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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