SMTL ID : 6xxk.1

Crystal Structure of Human Deoxyhypusine Synthase in complex with spermidine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-tetramer

Ligands

4 x SPD: SPERMIDINE(Non-covalent)

SPD.1: 17 residues within 4Å: Chain A: H.288, N.292, L.295, D.316, A.319, E.323, W.327, K.329 Chain B: G.133, E.136, R.165, I.166, Y.176, G.239, S.240, D.243 Chain C: V.17 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:W.327, A:W.327 Hydrogen bonds: A:N.292, A:D.316, A:E.323, A:K.329, B:D.243 Water bridges: B:E.136, B:D.243 SPD.24: 16 residues within 4Å: Chain A: E.136, R.165, I.166, 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: BME.14, EDO.31 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.327, B:W.327 Hydrogen bonds: B:N.292, B:E.323, B:K.329, A:D.243 SPD.42: 17 residues within 4Å: Chain A: V.17 Chain C: H.288, N.292, L.295, D.316, A.319, E.323, W.327, K.329 Chain D: G.133, E.136, R.165, I.166, Y.176, G.239, S.240, D.243 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:W.327, C:W.327 Hydrogen bonds: C:N.292, C:E.323, C:K.329, D:D.243 Water bridges: D:Y.176 SPD.65: 16 residues within 4Å: Chain C: E.136, R.165, I.166, 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: BME.55, EDO.72 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:W.327, D:W.327 Hydrogen bonds: D:N.292, D:D.316, D:E.323, D:K.329, C:D.243 Water bridges: C:D.243

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

EDO.2: 15 residues within 4Å: Chain A: T.104, N.106, L.107, G.282, G.283, I.306, N.307, T.308, A.341, D.342, A.343, S.344 Chain B: D.313, S.315 Ligands: EDO.8 Ligand excluded by PLIP EDO.3: 5 residues within 4Å: Chain A: P.185, I.186, Q.189, E.213 Ligands: FMT.22 Ligand excluded by PLIP EDO.4: 9 residues within 4Å: Chain A: S.90, R.91, R.92, A.208, A.224, Q.225, H.228, I.229, P.230 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: A.68, E.71, K.72, Y.302 Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain A: K.73, R.92, P.93, L.94, T.95, N.123, D.126 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: N.67, A.68, E.71, K.358 Ligand excluded by PLIP EDO.8: 11 residues within 4Å: Chain A: T.104, G.282, G.283, N.307, T.308, A.309, S.317 Chain B: D.313, S.315, S.317 Ligands: EDO.2 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: V.199, W.201, K.205 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain B: K.212, E.213, N.215 Ligand excluded by PLIP EDO.27: 7 residues within 4Å: Chain A: R.154 Chain B: R.61, R.320, P.321, D.322, P.336 Ligands: ACT.35 Ligand excluded by PLIP EDO.28: 15 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, S.344 Ligand excluded by PLIP EDO.29: 8 residues within 4Å: Chain B: R.32, G.33, Y.34, D.35, R.38, A.44, A.48, T.51 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain B: V.191, Q.194, N.195, P.253, G.254, L.255 Ligand excluded by PLIP EDO.31: 11 residues within 4Å: Chain B: K.287, Y.305, D.316, A.319, R.320, P.321, E.323, A.324, W.327, K.329 Ligands: SPD.24 Ligand excluded by PLIP EDO.43: 15 residues within 4Å: Chain C: T.104, N.106, L.107, G.282, G.283, I.306, N.307, T.308, A.341, D.342, A.343, S.344 Chain D: D.313, S.315 Ligands: EDO.49 Ligand excluded by PLIP EDO.44: 5 residues within 4Å: Chain C: P.185, I.186, Q.189, E.213 Ligands: FMT.63 Ligand excluded by PLIP EDO.45: 9 residues within 4Å: Chain C: S.90, R.91, R.92, A.208, A.224, Q.225, H.228, I.229, P.230 Ligand excluded by PLIP EDO.46: 4 residues within 4Å: Chain C: A.68, E.71, K.72, Y.302 Ligand excluded by PLIP EDO.47: 7 residues within 4Å: Chain C: K.73, R.92, P.93, L.94, T.95, N.123, D.126 Ligand excluded by PLIP EDO.48: 4 residues within 4Å: Chain C: N.67, A.68, E.71, K.358 Ligand excluded by PLIP EDO.49: 11 residues within 4Å: Chain C: T.104, G.282, G.283, N.307, T.308, A.309, S.317 Chain D: D.313, S.315, S.317 Ligands: EDO.43 Ligand excluded by PLIP EDO.50: 3 residues within 4Å: Chain C: V.199, W.201, K.205 Ligand excluded by PLIP EDO.67: 3 residues within 4Å: Chain D: K.212, E.213, N.215 Ligand excluded by PLIP EDO.68: 7 residues within 4Å: Chain C: R.154 Chain D: R.61, R.320, P.321, D.322, P.336 Ligands: ACT.76 Ligand excluded by PLIP EDO.69: 15 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, S.344 Ligand excluded by PLIP EDO.70: 8 residues within 4Å: Chain D: R.32, G.33, Y.34, D.35, R.38, A.44, A.48, T.51 Ligand excluded by PLIP EDO.71: 6 residues within 4Å: Chain D: V.191, Q.194, N.195, P.253, G.254, L.255 Ligand excluded by PLIP EDO.72: 11 residues within 4Å: Chain D: K.287, Y.305, D.316, A.319, R.320, P.321, E.323, A.324, W.327, K.329 Ligands: SPD.65 Ligand excluded by PLIP

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

ACT.10: 3 residues within 4Å: Chain A: E.180, F.247 Ligands: ACT.12 Ligand excluded by PLIP ACT.11: 5 residues within 4Å: Chain A: G.50, T.57, R.61, Q.64 Chain D: L.148 Ligand excluded by PLIP ACT.12: 4 residues within 4Å: Chain A: C.177, E.180, D.181 Ligands: ACT.10 Ligand excluded by PLIP ACT.13: 5 residues within 4Å: Chain A: Y.147, I.163, L.170, P.172 Chain D: S.28 Ligand excluded by PLIP ACT.32: 5 residues within 4Å: Chain B: C.142, L.143, W.182, I.214, N.216 Ligand excluded by PLIP ACT.33: 5 residues within 4Å: Chain A: F.246, F.247 Chain B: I.271, M.296 Ligands: FMT.40 Ligand excluded by PLIP ACT.34: 9 residues within 4Å: Chain A: S.105, T.131, G.133, D.238 Chain B: G.284, V.285, H.288, D.316, S.317 Ligand excluded by PLIP ACT.35: 8 residues within 4Å: Chain A: R.154 Chain B: R.61, R.320, D.322 Chain C: E.150, F.151, S.152 Ligands: EDO.27 Ligand excluded by PLIP ACT.36: 6 residues within 4Å: Chain B: K.141, C.142, L.143, A.144, P.145, E.218 Ligand excluded by PLIP ACT.51: 3 residues within 4Å: Chain C: E.180, F.247 Ligands: ACT.53 Ligand excluded by PLIP ACT.52: 5 residues within 4Å: Chain B: L.148 Chain C: G.50, T.57, R.61, Q.64 Ligand excluded by PLIP ACT.53: 4 residues within 4Å: Chain C: C.177, E.180, D.181 Ligands: ACT.51 Ligand excluded by PLIP ACT.54: 5 residues within 4Å: Chain B: S.28 Chain C: Y.147, I.163, L.170, P.172 Ligand excluded by PLIP ACT.73: 5 residues within 4Å: Chain D: C.142, L.143, W.182, I.214, N.216 Ligand excluded by PLIP ACT.74: 5 residues within 4Å: Chain C: F.246, F.247 Chain D: I.271, M.296 Ligands: FMT.81 Ligand excluded by PLIP ACT.75: 9 residues within 4Å: Chain C: S.105, T.131, G.133, D.238 Chain D: G.284, V.285, H.288, D.316, S.317 Ligand excluded by PLIP ACT.76: 8 residues within 4Å: Chain A: E.150, F.151, S.152 Chain C: R.154 Chain D: R.61, R.320, D.322 Ligands: EDO.68 Ligand excluded by PLIP ACT.77: 6 residues within 4Å: Chain D: K.141, C.142, L.143, A.144, P.145, E.218 Ligand excluded by PLIP

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

BME.14: 6 residues within 4Å: Chain A: N.164, N.173, Y.176 Chain B: L.295, W.327 Ligands: SPD.24 No protein-ligand interaction detected (PLIP) BME.15: 7 residues within 4Å: Chain A: L.87, T.88, Q.89, E.261, R.264, L.265, T.268 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.261, A:R.264, A:R.264 BME.16: 7 residues within 4Å: Chain A: C.142, L.143, W.182, I.214, N.215, N.216 Ligands: FMT.21 No protein-ligand interaction detected (PLIP) BME.37: 9 residues within 4Å: Chain B: G.149, E.150, F.151, S.152, N.168 Chain C: T.57, N.58, R.61 Ligands: FMT.60 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:N.58, C:R.61, B:N.168 Water bridges: B:G.149 BME.55: 6 residues within 4Å: Chain C: N.164, N.173, Y.176 Chain D: L.295, W.327 Ligands: SPD.65 1 PLIP interactions: 1 interactions with chain C Water bridges: C:D.243 BME.56: 7 residues within 4Å: Chain C: L.87, T.88, Q.89, E.261, R.264, L.265, T.268 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.261, C:R.264, C:R.264 BME.57: 7 residues within 4Å: Chain C: C.142, L.143, W.182, I.214, N.215, N.216 Ligands: FMT.62 No protein-ligand interaction detected (PLIP) BME.78: 9 residues within 4Å: Chain A: T.57, N.58, R.61 Chain D: G.149, E.150, F.151, S.152, N.168 Ligands: FMT.19 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:N.168, A:N.58, A:R.61 Water bridges: D:G.149

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

FMT.17: 7 residues within 4Å: Chain A: R.32, G.33, Y.34, D.35, R.38, A.48, T.51 Ligand excluded by PLIP FMT.18: 5 residues within 4Å: Chain A: E.311, F.312 Chain B: F.151 Chain C: R.320, Y.340 Ligand excluded by PLIP FMT.19: 6 residues within 4Å: Chain A: N.58, R.61, V.337, K.338, Y.340 Ligands: BME.78 Ligand excluded by PLIP FMT.20: 5 residues within 4Å: Chain A: S.21, S.22, T.23 Chain D: P.172, E.174 Ligand excluded by PLIP FMT.21: 4 residues within 4Å: Chain A: I.214, N.215, N.216 Ligands: BME.16 Ligand excluded by PLIP FMT.22: 5 residues within 4Å: Chain A: D.181, W.182, P.185, I.186 Ligands: EDO.3 Ligand excluded by PLIP FMT.23: 5 residues within 4Å: Chain A: Q.194, K.200, W.201, V.256 Chain B: V.256 Ligand excluded by PLIP FMT.38: 5 residues within 4Å: Chain B: A.208, Q.225, H.228, I.229, P.230 Ligand excluded by PLIP FMT.39: 4 residues within 4Å: Chain B: L.143, K.178, D.181, W.182 Ligand excluded by PLIP FMT.40: 5 residues within 4Å: Chain A: F.247 Chain B: L.295, M.296, N.298 Ligands: ACT.33 Ligand excluded by PLIP FMT.41: 5 residues within 4Å: Chain B: Q.64, Q.65, A.68, Y.302, Q.335 Ligand excluded by PLIP FMT.58: 7 residues within 4Å: Chain C: R.32, G.33, Y.34, D.35, R.38, A.48, T.51 Ligand excluded by PLIP FMT.59: 5 residues within 4Å: Chain A: R.320, Y.340 Chain C: E.311, F.312 Chain D: F.151 Ligand excluded by PLIP FMT.60: 6 residues within 4Å: Chain C: N.58, R.61, V.337, K.338, Y.340 Ligands: BME.37 Ligand excluded by PLIP FMT.61: 5 residues within 4Å: Chain B: P.172, E.174 Chain C: S.21, S.22, T.23 Ligand excluded by PLIP FMT.62: 4 residues within 4Å: Chain C: I.214, N.215, N.216 Ligands: BME.57 Ligand excluded by PLIP FMT.63: 5 residues within 4Å: Chain C: D.181, W.182, P.185, I.186 Ligands: EDO.44 Ligand excluded by PLIP FMT.64: 5 residues within 4Å: Chain C: Q.194, K.200, W.201, V.256 Chain D: V.256 Ligand excluded by PLIP FMT.79: 5 residues within 4Å: Chain D: A.208, Q.225, H.228, I.229, P.230 Ligand excluded by PLIP FMT.80: 4 residues within 4Å: Chain D: L.143, K.178, D.181, W.182 Ligand excluded by PLIP FMT.81: 5 residues within 4Å: Chain C: F.247 Chain D: L.295, M.296, N.298 Ligands: ACT.74 Ligand excluded by PLIP FMT.82: 5 residues within 4Å: Chain D: Q.64, Q.65, A.68, Y.302, Q.335 Ligand excluded by PLIP

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

MRD.25: 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 MRD.66: 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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