SMTL ID : 6xxi.1

Crystal Structure of Human Deoxyhypusine Synthase in complex with NAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

homo-tetramer

Ligands

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

ACT.1: 6 residues within 4Å: Chain A: K.141, C.142, L.143, A.144, P.145 Chain D: Q.30 Ligand excluded by PLIP ACT.3: 3 residues within 4Å: Chain A: K.212, E.213, N.215 Ligand excluded by PLIP ACT.4: 3 residues within 4Å: Chain A: V.199, W.201, K.205 Ligand excluded by PLIP ACT.9: 3 residues within 4Å: Chain A: M.184, H.248, K.251 Ligand excluded by PLIP ACT.10: 5 residues within 4Å: Chain A: Y.147, I.163, L.170, P.172 Chain D: S.28 Ligand excluded by PLIP ACT.11: 6 residues within 4Å: Chain A: C.142, L.143, W.182, I.214, N.215, N.216 Ligand excluded by PLIP ACT.12: 5 residues within 4Å: Chain A: S.28 Chain D: Y.147, I.163, L.170, P.172 Ligand excluded by PLIP ACT.24: 6 residues within 4Å: Chain B: P.217, Y.222, W.223, K.226 Ligands: EDO.30, EDO.42 Ligand excluded by PLIP ACT.25: 7 residues within 4Å: Chain B: K.141, C.142, A.144, P.145, E.218 Chain C: Q.30, R.32 Ligand excluded by PLIP ACT.27: 4 residues within 4Å: Chain B: K.212, E.213, N.215 Ligands: EDO.26 Ligand excluded by PLIP ACT.28: 5 residues within 4Å: Chain A: F.246, F.247 Chain B: I.271, M.296 Ligands: EDO.29 Ligand excluded by PLIP ACT.34: 5 residues within 4Å: Chain B: C.142, L.143, W.182, I.214, N.216 Ligand excluded by PLIP ACT.35: 4 residues within 4Å: Chain B: P.185, I.186, Q.189, E.213 Ligand excluded by PLIP ACT.36: 5 residues within 4Å: Chain A: I.271, F.272 Chain B: F.246, F.247, Y.250 Ligand excluded by PLIP ACT.41: 6 residues within 4Å: Chain B: Q.30 Chain C: K.141, C.142, L.143, A.144, P.145 Ligand excluded by PLIP ACT.43: 3 residues within 4Å: Chain C: K.212, E.213, N.215 Ligand excluded by PLIP ACT.44: 3 residues within 4Å: Chain C: V.199, W.201, K.205 Ligand excluded by PLIP ACT.49: 3 residues within 4Å: Chain C: M.184, H.248, K.251 Ligand excluded by PLIP ACT.50: 5 residues within 4Å: Chain B: S.28 Chain C: Y.147, I.163, L.170, P.172 Ligand excluded by PLIP ACT.51: 6 residues within 4Å: Chain C: C.142, L.143, W.182, I.214, N.215, N.216 Ligand excluded by PLIP ACT.52: 5 residues within 4Å: Chain B: Y.147, I.163, L.170, P.172 Chain C: S.28 Ligand excluded by PLIP ACT.64: 6 residues within 4Å: Chain D: P.217, Y.222, W.223, K.226 Ligands: EDO.2, EDO.70 Ligand excluded by PLIP ACT.65: 7 residues within 4Å: Chain A: Q.30, R.32 Chain D: K.141, C.142, A.144, P.145, E.218 Ligand excluded by PLIP ACT.67: 4 residues within 4Å: Chain D: K.212, E.213, N.215 Ligands: EDO.66 Ligand excluded by PLIP ACT.68: 5 residues within 4Å: Chain C: F.246, F.247 Chain D: I.271, M.296 Ligands: EDO.69 Ligand excluded by PLIP ACT.74: 5 residues within 4Å: Chain D: C.142, L.143, W.182, I.214, N.216 Ligand excluded by PLIP ACT.75: 4 residues within 4Å: Chain D: P.185, I.186, Q.189, E.213 Ligand excluded by PLIP ACT.76: 5 residues within 4Å: Chain C: I.271, F.272 Chain D: F.246, F.247, Y.250 Ligand excluded by PLIP

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

EDO.2: 7 residues within 4Å: Chain A: N.37 Chain D: R.117, Q.121, P.217, E.218, W.223 Ligands: ACT.64 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: A.208, A.224, Q.225, H.228, I.229, P.230 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: R.320, D.322 Chain B: S.152, R.154 Chain D: S.152 Ligands: EDO.21 Ligand excluded by PLIP EDO.15: 7 residues within 4Å: Chain A: R.32, G.33, Y.34, D.35, R.38, A.48, T.51 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain A: A.68, E.71, K.72, E.75, Y.302 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: V.191, M.192, N.195, T.196 Ligand excluded by PLIP EDO.18: 10 residues within 4Å: Chain A: H.288, N.292, L.295, W.327, K.329 Chain B: E.136, Y.176, G.239, S.240 Ligands: NAD.32 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain A: A.144, P.145, Y.147, P.172, E.174, N.175, K.178 Ligand excluded by PLIP EDO.20: 9 residues within 4Å: Chain A: R.43, L.46, E.47, F.49, G.50, F.59, G.60, V.63, E.353 Ligand excluded by PLIP EDO.21: 8 residues within 4Å: Chain A: N.58, R.61, P.321, P.336, V.337, K.338 Chain D: E.150 Ligands: EDO.14 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain B: A.208, A.224, Q.225, H.228, I.229, P.230 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain B: R.209, K.212, E.213 Ligands: ACT.27 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain B: I.271, M.296, R.297, N.298 Ligands: ACT.28 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain B: N.215, N.216, P.217, Y.222 Ligands: ACT.24 Ligand excluded by PLIP EDO.37: 3 residues within 4Å: Chain B: V.199, W.201, K.205 Ligand excluded by PLIP EDO.38: 5 residues within 4Å: Chain B: Q.64, N.67, A.68, E.71, K.358 Ligand excluded by PLIP EDO.39: 4 residues within 4Å: Chain B: Q.30, V.31, R.32 Ligands: BME.33 Ligand excluded by PLIP EDO.40: 11 residues within 4Å: Chain A: E.136, Y.176, G.239, S.240 Chain B: H.288, N.292, L.295, W.327, K.329 Ligands: NAD.5, BME.8 Ligand excluded by PLIP EDO.42: 7 residues within 4Å: Chain B: R.117, Q.121, P.217, E.218, W.223 Chain C: N.37 Ligands: ACT.24 Ligand excluded by PLIP EDO.53: 6 residues within 4Å: Chain C: A.208, A.224, Q.225, H.228, I.229, P.230 Ligand excluded by PLIP EDO.54: 6 residues within 4Å: Chain B: S.152 Chain C: R.320, D.322 Chain D: S.152, R.154 Ligands: EDO.61 Ligand excluded by PLIP EDO.55: 7 residues within 4Å: Chain C: R.32, G.33, Y.34, D.35, R.38, A.48, T.51 Ligand excluded by PLIP EDO.56: 5 residues within 4Å: Chain C: A.68, E.71, K.72, E.75, Y.302 Ligand excluded by PLIP EDO.57: 4 residues within 4Å: Chain C: V.191, M.192, N.195, T.196 Ligand excluded by PLIP EDO.58: 10 residues within 4Å: Chain C: H.288, N.292, L.295, W.327, K.329 Chain D: E.136, Y.176, G.239, S.240 Ligands: NAD.72 Ligand excluded by PLIP EDO.59: 7 residues within 4Å: Chain C: A.144, P.145, Y.147, P.172, E.174, N.175, K.178 Ligand excluded by PLIP EDO.60: 9 residues within 4Å: Chain C: R.43, L.46, E.47, F.49, G.50, F.59, G.60, V.63, E.353 Ligand excluded by PLIP EDO.61: 8 residues within 4Å: Chain B: E.150 Chain C: N.58, R.61, P.321, P.336, V.337, K.338 Ligands: EDO.54 Ligand excluded by PLIP EDO.63: 6 residues within 4Å: Chain D: A.208, A.224, Q.225, H.228, I.229, P.230 Ligand excluded by PLIP EDO.66: 4 residues within 4Å: Chain D: R.209, K.212, E.213 Ligands: ACT.67 Ligand excluded by PLIP EDO.69: 5 residues within 4Å: Chain D: I.271, M.296, R.297, N.298 Ligands: ACT.68 Ligand excluded by PLIP EDO.70: 5 residues within 4Å: Chain D: N.215, N.216, P.217, Y.222 Ligands: ACT.64 Ligand excluded by PLIP EDO.77: 3 residues within 4Å: Chain D: V.199, W.201, K.205 Ligand excluded by PLIP EDO.78: 5 residues within 4Å: Chain D: Q.64, N.67, A.68, E.71, K.358 Ligand excluded by PLIP EDO.79: 4 residues within 4Å: Chain D: Q.30, V.31, R.32 Ligands: BME.73 Ligand excluded by PLIP EDO.80: 11 residues within 4Å: Chain C: E.136, Y.176, G.239, S.240 Chain D: H.288, N.292, L.295, W.327, K.329 Ligands: NAD.45, BME.48 Ligand excluded by PLIP

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

NAD.5: 40 residues within 4Å: Chain A: T.104, S.105, N.106, L.107, S.109, T.131, A.132, G.133, G.134, E.136, E.137, I.166, A.235, 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.32, EDO.40 24 PLIP interactions: 15 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:S.105, A:S.105, A:N.106, A:T.131, A:T.131, A:A.132, A:G.133, A:D.238, A:G.283, A:T.308, A:D.342, A:A.343, B:G.284, B:D.316, B:S.317, B:S.317, B:S.317 Water bridges: A:N.106, A:N.106, A:G.283, B:V.285, B:G.314, B:S.315, B:D.316 NAD.32: 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, G.134, E.136, E.137, I.166, A.235, 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 C: F.54 Ligands: NAD.5, EDO.18 26 PLIP interactions: 18 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:S.105, B:S.105, B:N.106, B:T.131, B:T.131, B:A.132, B:G.133, B:E.137, B:D.238, B:G.283, B:T.308, B:D.342, B:A.343, A:G.284, A:S.315, A:D.316, A:S.317, A:S.317 Water bridges: B:N.106, B:N.106, B:G.283, B:V.285, B:T.308, A:V.285, A:S.315, A:D.316 NAD.45: 40 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, G.134, E.136, E.137, I.166, A.235, 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.72, EDO.80 26 PLIP interactions: 11 interactions with chain D, 15 interactions with chain C Hydrogen bonds: D:G.284, D:D.316, D:S.317, D:S.317, D:S.317, C:S.105, C:S.105, C:N.106, C:T.131, C:T.131, C:A.132, C:G.133, C:G.283, C:T.308, C:D.342, C:D.342, C:A.343 Water bridges: D:V.285, D:G.314, D:S.315, D:D.316, D:D.316, D:D.316, C:N.106, C:N.106, C:G.283 NAD.72: 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, G.134, E.136, E.137, I.166, A.235, 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 Ligands: NAD.45, EDO.58 26 PLIP interactions: 18 interactions with chain D, 8 interactions with chain C Hydrogen bonds: D:S.105, D:S.105, D:N.106, 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:S.315, C:D.316, C:S.317, C:S.317 Water bridges: D:N.106, D:N.106, D:G.283, D:V.285, D:T.308, C:V.285, C:S.315, C:D.316

8 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.264, A:R.264 BME.7: 4 residues within 4Å: Chain A: C.177, E.180, M.244, F.247 No protein-ligand interaction detected (PLIP) BME.8: 7 residues within 4Å: Chain A: Y.176, S.240, D.243, M.244 Chain B: L.295, W.327 Ligands: EDO.40 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.164 BME.33: 7 residues within 4Å: Chain B: R.32, Y.34, D.35, R.38, A.48, T.51 Ligands: EDO.39 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.50 BME.46: 8 residues within 4Å: Chain C: L.87, T.88, Q.89, E.261, R.264, L.265, T.268 Chain D: Y.250 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.264, C:R.264 BME.47: 4 residues within 4Å: Chain C: C.177, E.180, M.244, F.247 No protein-ligand interaction detected (PLIP) BME.48: 7 residues within 4Å: Chain C: Y.176, S.240, D.243, M.244 Chain D: L.295, W.327 Ligands: EDO.80 1 PLIP interactions: 1 interactions with chain C Water bridges: C:N.164 BME.73: 7 residues within 4Å: Chain D: R.32, Y.34, D.35, R.38, A.48, T.51 Ligands: EDO.79 1 PLIP interactions: 1 interactions with chain D Water bridges: D:G.50

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

FMT.22: 3 residues within 4Å: Chain A: D.35, N.37, R.38 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.35 FMT.62: 3 residues within 4Å: Chain C: D.35, N.37, R.38 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.35, C:D.35

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

MRD.31: 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.71: 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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