SMTL ID : 8qzw.1

Crystal structure of deoxyhypusine synthase from Trichomonas vaginalis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 38 residues within 4Å: Chain A: T.107, S.108, N.109, L.110, S.112, T.134, A.135, G.136, E.139, E.140, I.169, A.238, D.241, G.242, S.243, G.285, G.286, G.287, V.309, N.310, T.311, A.312, S.320, A.344, E.345, V.346, T.347 Chain C: G.287, V.288, H.291, A.312, D.316, G.317, S.318, D.319, S.320 Chain D: F.53 Ligands: NAD.25 24 PLIP interactions: 17 interactions with chain A, 7 interactions with chain C Hydrogen bonds: A:S.108, A:S.108, A:S.108, A:N.109, A:T.134, A:A.135, A:G.136, A:G.286, A:T.311, A:T.311, A:E.345, A:V.346, C:G.287, C:D.316, C:D.319, C:S.320, C:S.320, C:S.320 Water bridges: A:N.109, A:N.109, A:V.288, A:V.288, A:T.311, C:D.316 NAD.13: 38 residues within 4Å: Chain B: T.107, S.108, N.109, L.110, S.112, T.134, A.135, G.136, E.139, E.140, I.169, A.238, D.241, G.242, S.243, G.285, G.286, G.287, V.309, N.310, T.311, A.312, S.320, A.344, E.345, V.346, T.347 Chain C: F.53 Chain D: G.287, V.288, H.291, A.312, D.316, G.317, S.318, D.319, S.320 Ligands: NAD.37 24 PLIP interactions: 17 interactions with chain B, 7 interactions with chain D Hydrogen bonds: B:S.108, B:S.108, B:S.108, B:N.109, B:T.134, B:A.135, B:G.136, B:D.241, B:G.286, B:T.311, B:T.311, B:V.346, D:G.287, D:D.316, D:D.319, D:S.320, D:S.320, D:S.320 Water bridges: B:N.109, B:N.109, B:V.288, B:V.288, B:T.311, D:D.316 NAD.25: 38 residues within 4Å: Chain A: G.287, V.288, H.291, A.312, D.316, G.317, S.318, D.319, S.320 Chain B: F.53 Chain C: T.107, S.108, N.109, L.110, S.112, T.134, A.135, G.136, E.139, E.140, I.169, A.238, D.241, G.242, S.243, G.285, G.286, G.287, V.309, N.310, T.311, A.312, S.320, A.344, E.345, V.346, T.347 Ligands: NAD.1 24 PLIP interactions: 7 interactions with chain A, 17 interactions with chain C Hydrogen bonds: A:G.287, A:D.316, A:D.319, A:S.320, A:S.320, A:S.320, C:S.108, C:S.108, C:S.108, C:N.109, C:T.134, C:A.135, C:G.136, C:G.286, C:T.311, C:T.311, C:E.345, C:V.346 Water bridges: A:D.316, C:N.109, C:N.109, C:V.288, C:V.288, C:T.311 NAD.37: 38 residues within 4Å: Chain A: F.53 Chain B: G.287, V.288, H.291, A.312, D.316, G.317, S.318, D.319, S.320 Chain D: T.107, S.108, N.109, L.110, S.112, T.134, A.135, G.136, E.139, E.140, I.169, A.238, D.241, G.242, S.243, G.285, G.286, G.287, V.309, N.310, T.311, A.312, S.320, A.344, E.345, V.346, T.347 Ligands: NAD.13 24 PLIP interactions: 17 interactions with chain D, 7 interactions with chain B Hydrogen bonds: D:S.108, D:S.108, D:S.108, D:N.109, D:T.134, D:A.135, D:G.136, D:D.241, D:G.286, D:T.311, D:T.311, D:V.346, B:G.287, B:D.316, B:D.319, B:S.320, B:S.320, B:S.320 Water bridges: D:N.109, D:N.109, D:V.288, D:V.288, D:T.311, B:D.316

28 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: R.323, P.324, D.325, P.339 Chain D: F.155 Ligand excluded by PLIP SO4.3: 4 residues within 4Å: Chain A: E.153, F.154, F.155, N.171 Ligand excluded by PLIP SO4.4: 5 residues within 4Å: Chain A: D.72, K.81, L.83, P.97, A.99 Ligand excluded by PLIP SO4.5: 4 residues within 4Å: Chain A: N.218, N.219, E.220, Y.225 Ligand excluded by PLIP SO4.6: 11 residues within 4Å: Chain A: T.311, H.313 Chain B: H.313, F.315 Chain C: H.313, F.315 Chain D: T.311, H.313 Ligands: SO4.18, SO4.30, SO4.42 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain A: H.156, R.164 Ligands: GOL.10 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain A: C.145, L.146, I.217, N.219 Ligand excluded by PLIP SO4.14: 5 residues within 4Å: Chain B: R.323, P.324, D.325, P.339 Chain C: F.155 Ligand excluded by PLIP SO4.15: 4 residues within 4Å: Chain B: E.153, F.154, F.155, N.171 Ligand excluded by PLIP SO4.16: 5 residues within 4Å: Chain B: D.72, K.81, L.83, P.97, A.99 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain B: N.218, N.219, E.220, Y.225 Ligand excluded by PLIP SO4.18: 11 residues within 4Å: Chain A: H.313, F.315 Chain B: T.311, H.313 Chain C: T.311, H.313 Chain D: H.313, F.315 Ligands: SO4.6, SO4.30, SO4.42 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain B: H.156, R.164 Ligands: GOL.22 Ligand excluded by PLIP SO4.20: 4 residues within 4Å: Chain B: C.145, L.146, I.217, N.219 Ligand excluded by PLIP SO4.26: 5 residues within 4Å: Chain B: F.155 Chain C: R.323, P.324, D.325, P.339 Ligand excluded by PLIP SO4.27: 4 residues within 4Å: Chain C: E.153, F.154, F.155, N.171 Ligand excluded by PLIP SO4.28: 5 residues within 4Å: Chain C: D.72, K.81, L.83, P.97, A.99 Ligand excluded by PLIP SO4.29: 4 residues within 4Å: Chain C: N.218, N.219, E.220, Y.225 Ligand excluded by PLIP SO4.30: 11 residues within 4Å: Chain A: H.313, F.315 Chain B: T.311, H.313 Chain C: T.311, H.313 Chain D: H.313, F.315 Ligands: SO4.6, SO4.18, SO4.42 Ligand excluded by PLIP SO4.31: 3 residues within 4Å: Chain C: H.156, R.164 Ligands: GOL.34 Ligand excluded by PLIP SO4.32: 4 residues within 4Å: Chain C: C.145, L.146, I.217, N.219 Ligand excluded by PLIP SO4.38: 5 residues within 4Å: Chain A: F.155 Chain D: R.323, P.324, D.325, P.339 Ligand excluded by PLIP SO4.39: 4 residues within 4Å: Chain D: E.153, F.154, F.155, N.171 Ligand excluded by PLIP SO4.40: 5 residues within 4Å: Chain D: D.72, K.81, L.83, P.97, A.99 Ligand excluded by PLIP SO4.41: 4 residues within 4Å: Chain D: N.218, N.219, E.220, Y.225 Ligand excluded by PLIP SO4.42: 11 residues within 4Å: Chain A: T.311, H.313 Chain B: H.313, F.315 Chain C: H.313, F.315 Chain D: T.311, H.313 Ligands: SO4.6, SO4.18, SO4.30 Ligand excluded by PLIP SO4.43: 3 residues within 4Å: Chain D: H.156, R.164 Ligands: GOL.46 Ligand excluded by PLIP SO4.44: 4 residues within 4Å: Chain D: C.145, L.146, I.217, N.219 Ligand excluded by PLIP

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 10 residues within 4Å: Chain A: K.290, H.291, M.294, Y.308, D.319, A.322, E.326, A.327, W.330, K.332 Ligand excluded by PLIP GOL.10: 10 residues within 4Å: Chain A: G.152, E.153, H.156, L.161, R.164, L.166, I.173 Chain D: L.23, T.25 Ligands: SO4.7 Ligand excluded by PLIP GOL.11: 6 residues within 4Å: Chain A: R.120, K.124, E.220, D.221, W.226 Chain D: V.32 Ligand excluded by PLIP GOL.12: 5 residues within 4Å: Chain A: P.188, I.189, K.192, R.212, E.216 Ligand excluded by PLIP GOL.21: 10 residues within 4Å: Chain B: K.290, H.291, M.294, Y.308, D.319, A.322, E.326, A.327, W.330, K.332 Ligand excluded by PLIP GOL.22: 10 residues within 4Å: Chain B: G.152, E.153, H.156, L.161, R.164, L.166, I.173 Chain C: L.23, T.25 Ligands: SO4.19 Ligand excluded by PLIP GOL.23: 6 residues within 4Å: Chain B: R.120, K.124, E.220, D.221, W.226 Chain C: V.32 Ligand excluded by PLIP GOL.24: 5 residues within 4Å: Chain B: P.188, I.189, K.192, R.212, E.216 Ligand excluded by PLIP GOL.33: 10 residues within 4Å: Chain C: K.290, H.291, M.294, Y.308, D.319, A.322, E.326, A.327, W.330, K.332 Ligand excluded by PLIP GOL.34: 10 residues within 4Å: Chain B: L.23, T.25 Chain C: G.152, E.153, H.156, L.161, R.164, L.166, I.173 Ligands: SO4.31 Ligand excluded by PLIP GOL.35: 6 residues within 4Å: Chain B: V.32 Chain C: R.120, K.124, E.220, D.221, W.226 Ligand excluded by PLIP GOL.36: 5 residues within 4Å: Chain C: P.188, I.189, K.192, R.212, E.216 Ligand excluded by PLIP GOL.45: 10 residues within 4Å: Chain D: K.290, H.291, M.294, Y.308, D.319, A.322, E.326, A.327, W.330, K.332 Ligand excluded by PLIP GOL.46: 10 residues within 4Å: Chain A: L.23, T.25 Chain D: G.152, E.153, H.156, L.161, R.164, L.166, I.173 Ligands: SO4.43 Ligand excluded by PLIP GOL.47: 6 residues within 4Å: Chain A: V.32 Chain D: R.120, K.124, E.220, D.221, W.226 Ligand excluded by PLIP GOL.48: 5 residues within 4Å: Chain D: P.188, I.189, K.192, R.212, E.216 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wator, E. et al., Structural characterization of the (deoxy)hypusination in Trichomonas vaginalis questions the bifunctionality of deoxyhypusine synthase. Febs J. (2024)

Release Date

2024-07-03

Peptides

Deoxyhypusine synthase related protein, putative: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Deoxyhypusine synthase related protein, putative