SMTL ID : 6xxl.1

Crystal Structure of Human Deoxyhypusine Synthase in complex with spermine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

homo-tetramer

Ligands

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.1: 10 residues within 4Å: Chain A: L.263, I.266, N.267, H.289, N.292, A.293 Chain B: T.237, D.238, G.239, D.243 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:D.238, B:G.239, A:H.289, A:N.292 Water bridges: A:N.267, A:N.267 FMT.21: 10 residues within 4Å: Chain C: L.263, I.266, N.267, H.289, N.292, A.293 Chain D: T.237, D.238, G.239, D.243 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:H.289, C:N.292, D:D.238, D:D.238, D:G.239 Water bridges: C:N.267, C:N.267

4 x SPM: SPERMINE(Non-covalent)

SPM.2: 17 residues within 4Å: Chain A: H.288, N.292, L.295, D.316, A.319, E.323, W.327, K.329 Chain B: R.159, N.164, R.165, I.166, N.173, Y.176, G.239, S.240, D.243 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:H.288, A:D.316, A:E.323, A:K.329, B:N.173, B:S.240 Water bridges: B:R.159, B:D.243 SPM.15: 18 residues within 4Å: Chain A: E.136, R.159, N.164, R.165, I.166, N.173, 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 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:W.327 Hydrogen bonds: B:H.288, B:D.316, B:K.329, A:N.173, A:S.240 Water bridges: A:E.137, A:R.159, A:N.164 SPM.22: 17 residues within 4Å: Chain C: H.288, N.292, L.295, D.316, A.319, E.323, W.327, K.329 Chain D: R.159, N.164, R.165, I.166, N.173, Y.176, G.239, S.240, D.243 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:N.173, D:S.240, C:H.288, C:E.323, C:K.329 Water bridges: D:R.159 SPM.35: 18 residues within 4Å: Chain C: E.136, R.159, N.164, R.165, I.166, N.173, 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 9 PLIP interactions: 5 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:W.327 Hydrogen bonds: D:H.288, D:D.316, D:D.316, D:K.329, C:N.173, C:S.240 Water bridges: C:R.159, C:N.164

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

EDO.3: 14 residues within 4Å: Chain A: D.313, S.315 Chain B: T.104, N.106, L.107, L.281, G.282, G.283, I.306, N.307, T.308, A.341, D.342, A.343 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.106, B:N.106, B:A.343 Water bridges: B:T.308, B:S.344 EDO.4: 14 residues within 4Å: Chain A: T.104, N.106, L.107, L.281, G.282, I.306, N.307, T.308, A.341, D.342, A.343, S.344 Chain B: D.313, S.315 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.106, A:N.106, A:A.343 EDO.16: 6 residues within 4Å: Chain B: A.208, A.224, Q.225, H.228, I.229, P.230 2 PLIP interactions: 2 interactions with chain B Water bridges: B:A.224, B:I.229 EDO.17: 7 residues within 4Å: Chain B: R.113, E.114, R.117, K.141, E.218 Chain C: V.31, R.32 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:R.113 Water bridges: B:R.113, B:R.113, B:E.114, B:R.117, C:V.31 EDO.23: 14 residues within 4Å: Chain C: D.313, S.315 Chain D: T.104, N.106, L.107, L.281, G.282, G.283, I.306, N.307, T.308, A.341, D.342, A.343 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:N.106, D:N.106, D:D.342, D:A.343 Water bridges: D:T.308, D:S.344 EDO.24: 14 residues within 4Å: Chain C: T.104, N.106, L.107, L.281, G.282, I.306, N.307, T.308, A.341, D.342, A.343, S.344 Chain D: D.313, S.315 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain C Water bridges: D:D.313 Hydrogen bonds: C:N.106, C:N.106, C:D.342, C:A.343 EDO.36: 6 residues within 4Å: Chain D: A.208, A.224, Q.225, H.228, I.229, P.230 2 PLIP interactions: 2 interactions with chain D Water bridges: D:A.224, D:I.229 EDO.37: 7 residues within 4Å: Chain A: V.31, R.32 Chain D: R.113, E.114, R.117, K.141, E.218 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain D Water bridges: A:V.31, D:R.113, D:R.113, D:E.114, D:E.114 Hydrogen bonds: D:R.113

4 x OXM: OXAMIC ACID(Non-covalent)

OXM.5: 6 residues within 4Å: Chain A: C.142, L.143, W.182, I.214, N.215, N.216 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.214, A:N.216 Water bridges: A:W.182 OXM.6: 7 residues within 4Å: Chain A: G.50, T.51, T.57, G.60, R.61, Q.64 Chain D: L.148 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.64 OXM.25: 6 residues within 4Å: Chain C: C.142, L.143, W.182, I.214, N.215, N.216 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:I.214, C:N.216 Water bridges: C:W.182 OXM.26: 7 residues within 4Å: Chain B: L.148 Chain C: G.50, T.51, T.57, G.60, R.61, Q.64 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.64

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

ACT.7: 4 residues within 4Å: Chain A: S.28 Chain D: Y.147, I.163, L.170 Ligand excluded by PLIP ACT.8: 4 residues within 4Å: Chain A: C.177, E.180, M.244, F.247 Ligand excluded by PLIP ACT.9: 5 residues within 4Å: Chain A: Y.147, I.163, L.170, P.172 Chain D: S.28 Ligand excluded by PLIP ACT.10: 5 residues within 4Å: Chain A: K.141, C.142, L.143, A.144, P.145 Ligand excluded by PLIP ACT.11: 3 residues within 4Å: Chain A: D.35, N.37, R.38 Ligand excluded by PLIP ACT.12: 1 residues within 4Å: Chain A: F.272 Ligand excluded by PLIP ACT.18: 4 residues within 4Å: Chain B: P.217, Y.222, W.223, K.226 Ligand excluded by PLIP ACT.19: 7 residues within 4Å: Chain B: K.73, L.74, T.95, N.123, A.361, F.362, H.364 Ligand excluded by PLIP ACT.20: 3 residues within 4Å: Chain B: K.212, E.213, N.215 Ligand excluded by PLIP ACT.27: 4 residues within 4Å: Chain B: Y.147, I.163, L.170 Chain C: S.28 Ligand excluded by PLIP ACT.28: 4 residues within 4Å: Chain C: C.177, E.180, M.244, F.247 Ligand excluded by PLIP ACT.29: 5 residues within 4Å: Chain B: S.28 Chain C: Y.147, I.163, L.170, P.172 Ligand excluded by PLIP ACT.30: 5 residues within 4Å: Chain C: K.141, C.142, L.143, A.144, P.145 Ligand excluded by PLIP ACT.31: 3 residues within 4Å: Chain C: D.35, N.37, R.38 Ligand excluded by PLIP ACT.32: 1 residues within 4Å: Chain C: F.272 Ligand excluded by PLIP ACT.38: 4 residues within 4Å: Chain D: P.217, Y.222, W.223, K.226 Ligand excluded by PLIP ACT.39: 7 residues within 4Å: Chain D: K.73, L.74, T.95, N.123, A.361, F.362, H.364 Ligand excluded by PLIP ACT.40: 3 residues within 4Å: Chain D: K.212, E.213, N.215 Ligand excluded by PLIP

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

BME.13: 8 residues within 4Å: Chain A: L.87, T.88, Q.89, E.261, R.264, L.265, T.268 Chain B: Y.250 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:L.87, A:R.264, B:Y.250 BME.33: 8 residues within 4Å: Chain C: L.87, T.88, Q.89, E.261, R.264, L.265, T.268 Chain D: Y.250 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:L.87, C:R.264, D:Y.250

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.14: 4 residues within 4Å: Chain B: R.38, G.39, V.40, N.41 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.38 Water bridges: B:V.40 MPD.34: 4 residues within 4Å: Chain D: R.38, G.39, V.40, N.41 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.38 Water bridges: D:V.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wator, E. et al., Half Way to Hypusine-Structural Basis for Substrate Recognition by Human Deoxyhypusine Synthase. Biomolecules (2020)

Release Date

2020-04-15

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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