SMTL ID : 6xxj.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.41 Å

Oligo State

homo-tetramer

Ligands

4 x SPD: SPERMIDINE(Non-covalent)

SPD.1: 12 residues within 4Å: Chain A: H.288, N.292, L.295, D.316, E.323, W.327, K.329 Chain B: I.166, S.240, D.243 Ligands: FMT.13, NAD.18 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.327, A:W.327 Hydrogen bonds: A:N.292, A:D.316, A:D.316, A:K.329, B:D.243 Water bridges: B:D.243 SPD.15: 13 residues within 4Å: Chain A: G.239, S.240, D.243 Chain B: H.288, N.292, L.295, D.316, E.323, W.327, K.329 Ligands: NAD.2, BME.9, FMT.27 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.327 Hydrogen bonds: B:N.292, B:D.316, B:K.329, A:D.243 SPD.30: 12 residues within 4Å: Chain C: H.288, N.292, L.295, D.316, E.323, W.327, K.329 Chain D: I.166, S.240, D.243 Ligands: FMT.42, NAD.47 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:W.327, C:W.327 Hydrogen bonds: C:N.292, C:D.316, C:K.329, D:D.243 SPD.44: 13 residues within 4Å: Chain C: G.239, S.240, D.243 Chain D: H.288, N.292, L.295, D.316, E.323, W.327, K.329 Ligands: NAD.31, BME.38, FMT.56 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:W.327 Hydrogen bonds: D:N.292, D:D.316, D:D.316, D:K.329, C:D.243 Water bridges: C:D.243

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

NAD.2: 31 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.282, G.283, I.306, N.307, T.308, A.309, A.341, D.342, A.343 Chain B: G.284, V.285, H.288, D.313, S.315, D.316, S.317 Ligands: SPD.15, NAD.18, FMT.27 24 PLIP interactions: 8 interactions with chain B, 16 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:S.105, A:N.106, A:S.109, A:T.131, A:T.131, A:A.132, A:G.133, A:E.137, A:D.238, A:G.283, A:T.308, A:D.342, A:A.343 Water bridges: B:V.285, B:D.316, A:N.106, A:N.106 NAD.18: 31 residues within 4Å: Chain A: G.284, V.285, H.288, 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, D.238, G.282, G.283, I.306, N.307, T.308, A.309, A.341, D.342, A.343 Ligands: SPD.1, NAD.2, FMT.13 21 PLIP interactions: 7 interactions with chain A, 14 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:S.105, B:N.106, B:S.109, B:T.131, B:A.132, B:G.133, B:E.137, B:D.238, B:G.283, B:T.308, B:T.308, B:D.342, B:A.343 Water bridges: A:V.285, A:S.315 NAD.31: 31 residues within 4Å: 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.282, G.283, I.306, N.307, T.308, A.309, A.341, D.342, A.343 Chain D: G.284, V.285, H.288, D.313, S.315, D.316, S.317 Ligands: SPD.44, NAD.47, FMT.56 25 PLIP interactions: 18 interactions with chain C, 7 interactions with chain D Hydrogen bonds: C:T.104, C:S.105, C:S.105, C:N.106, C:S.109, C:T.131, C:T.131, C:A.132, C:G.133, C:E.137, C:G.283, C:T.308, C:T.308, C:D.342, C:D.342, C:A.343, D:G.284, D:D.316, D:S.317, D:S.317, D:S.317, D:S.317 Water bridges: C:N.106, C:N.106, D:V.285 NAD.47: 31 residues within 4Å: Chain C: G.284, V.285, H.288, 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, D.238, G.282, G.283, I.306, N.307, T.308, A.309, A.341, D.342, A.343 Ligands: SPD.30, NAD.31, FMT.42 23 PLIP interactions: 16 interactions with chain D, 7 interactions with chain C Hydrogen bonds: D:T.104, D:S.105, D:S.105, D:N.106, D:S.109, D:T.131, D:T.131, D:A.132, D:G.133, D:E.137, 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:T.308, C:V.285, C:D.316

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

EDO.3: 3 residues within 4Å: Chain A: E.160, N.161, G.162 Ligand excluded by PLIP EDO.4: 2 residues within 4Å: Chain A: S.22, T.23 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: Q.194, V.199, K.200, V.256 Chain B: V.256 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain A: E.150, S.152, L.153 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain B: A.208, Q.225, H.228, I.229, P.230 Ligands: EDO.21 Ligand excluded by PLIP EDO.19: 2 residues within 4Å: Chain B: I.271, M.296 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain B: K.212, E.213, N.215 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain B: P.230, F.232, L.265, Q.269 Ligands: EDO.16 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain B: R.43, A.356, Q.357 Ligand excluded by PLIP EDO.32: 3 residues within 4Å: Chain C: E.160, N.161, G.162 Ligand excluded by PLIP EDO.33: 2 residues within 4Å: Chain C: S.22, T.23 Ligand excluded by PLIP EDO.34: 5 residues within 4Å: Chain C: Q.194, V.199, K.200, V.256 Chain D: V.256 Ligand excluded by PLIP EDO.35: 3 residues within 4Å: Chain C: E.150, S.152, L.153 Ligand excluded by PLIP EDO.45: 6 residues within 4Å: Chain D: A.208, Q.225, H.228, I.229, P.230 Ligands: EDO.50 Ligand excluded by PLIP EDO.48: 2 residues within 4Å: Chain D: I.271, M.296 Ligand excluded by PLIP EDO.49: 3 residues within 4Å: Chain D: K.212, E.213, N.215 Ligand excluded by PLIP EDO.50: 5 residues within 4Å: Chain D: P.230, F.232, L.265, Q.269 Ligands: EDO.45 Ligand excluded by PLIP EDO.51: 3 residues within 4Å: Chain D: R.43, A.356, Q.357 Ligand excluded by PLIP

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

ACT.7: 3 residues within 4Å: Chain A: A.85, Q.89, R.91 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.85 Hydrogen bonds: A:Q.89 ACT.24: 3 residues within 4Å: Chain B: C.142, I.214, N.216 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.216 ACT.25: 3 residues within 4Å: Chain B: N.215, P.217 Ligands: PGE.29 No protein-ligand interaction detected (PLIP) ACT.26: 4 residues within 4Å: Chain B: K.141, L.143, A.144, P.145 No protein-ligand interaction detected (PLIP) ACT.36: 3 residues within 4Å: Chain C: A.85, Q.89, R.91 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:A.85 Hydrogen bonds: C:Q.89 ACT.53: 3 residues within 4Å: Chain D: C.142, I.214, N.216 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.216 ACT.54: 3 residues within 4Å: Chain D: N.215, P.217 Ligands: PGE.58 No protein-ligand interaction detected (PLIP) ACT.55: 4 residues within 4Å: Chain D: K.141, L.143, A.144, P.145 No protein-ligand interaction detected (PLIP)

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

BME.8: 5 residues within 4Å: Chain A: N.58, R.61, P.336, V.337, K.338 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.61, A:R.61, A:K.338, A:K.338 Water bridges: A:N.58 BME.9: 4 residues within 4Å: Chain A: Y.176 Chain B: L.295, W.327 Ligands: SPD.15 No protein-ligand interaction detected (PLIP) BME.10: 7 residues within 4Å: Chain A: L.87, T.88, Q.89, E.261, R.264, L.265, T.268 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.261, A:R.264 BME.11: 4 residues within 4Å: Chain A: C.142, L.143, I.214, N.216 No protein-ligand interaction detected (PLIP) BME.37: 5 residues within 4Å: Chain C: N.58, R.61, P.336, V.337, K.338 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.61, C:R.61, C:K.338, C:K.338 Water bridges: C:N.58 BME.38: 4 residues within 4Å: Chain C: Y.176 Chain D: L.295, W.327 Ligands: SPD.44 2 PLIP interactions: 2 interactions with chain C Water bridges: C:D.243, C:D.243 BME.39: 7 residues within 4Å: Chain C: L.87, T.88, Q.89, E.261, R.264, L.265, T.268 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.261, C:R.264 BME.40: 4 residues within 4Å: Chain C: C.142, L.143, I.214, N.216 No protein-ligand interaction detected (PLIP)

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

FMT.12: 3 residues within 4Å: Chain A: N.298, G.328 Chain B: R.159 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.298, B:R.159 Water bridges: A:G.328, A:V.332, B:R.159 FMT.13: 9 residues within 4Å: Chain A: G.314, S.315, D.316, E.323 Chain B: N.106, I.166, G.167 Ligands: SPD.1, NAD.18 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.167 FMT.14: 6 residues within 4Å: Chain A: R.32, G.33, Y.34, R.38, A.48, T.51 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.32, A:R.38, A:T.51 FMT.27: 9 residues within 4Å: Chain A: N.106, I.166, G.167 Chain B: G.314, S.315, D.316, E.323 Ligands: NAD.2, SPD.15 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.323, A:G.167 Water bridges: A:N.106 FMT.28: 4 residues within 4Å: Chain B: K.73, L.74, A.361, F.362 No protein-ligand interaction detected (PLIP) FMT.41: 3 residues within 4Å: Chain C: N.298, G.328 Chain D: R.159 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:N.298, D:R.159 Water bridges: C:G.328, C:V.332, D:R.159 FMT.42: 9 residues within 4Å: Chain C: G.314, S.315, D.316, E.323 Chain D: N.106, I.166, G.167 Ligands: SPD.30, NAD.47 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.167 FMT.43: 6 residues within 4Å: Chain C: R.32, G.33, Y.34, R.38, A.48, T.51 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.32, C:R.38 FMT.56: 9 residues within 4Å: Chain C: N.106, I.166, G.167 Chain D: G.314, S.315, D.316, E.323 Ligands: NAD.31, SPD.44 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.167, D:E.323 Water bridges: C:N.106 FMT.57: 4 residues within 4Å: Chain D: K.73, L.74, A.361, F.362 No protein-ligand interaction detected (PLIP)

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

MRD.17: 3 residues within 4Å: Chain B: R.38, G.39, V.40 1 PLIP interactions: 1 interactions with chain B Water bridges: B:V.40 MRD.46: 3 residues within 4Å: Chain D: R.38, G.39, V.40 1 PLIP interactions: 1 interactions with chain D Water bridges: D:V.40

2 x OXM: OXAMIC ACID(Non-covalent)

OXM.23: 2 residues within 4Å: Chain B: S.28 Chain C: Y.147 No protein-ligand interaction detected (PLIP) OXM.52: 2 residues within 4Å: Chain A: Y.147 Chain D: S.28 No protein-ligand interaction detected (PLIP)

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.29: 6 residues within 4Å: Chain B: Q.121, P.217, Y.222, W.223, K.226 Ligands: ACT.25 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Water bridges: C:N.37 Hydrogen bonds: B:Q.121 PGE.58: 6 residues within 4Å: Chain D: Q.121, P.217, Y.222, W.223, K.226 Ligands: ACT.54 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:Q.121, D:Y.222 Water bridges: A:N.37

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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