SMTL ID : 1rqd.1

deoxyhypusine synthase holoenzyme in its low ionic strength, high pH crystal form with the inhibitor GC7 bound in the active site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 29 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, 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: NAD.7, GC7.8 19 PLIP interactions: 13 interactions with chain A, 6 interactions with chain D Hydrogen bonds: A:S.105, A:S.105, A:N.106, A:S.109, A:A.132, A:G.133, A:D.238, A:G.283, A:T.308, A:T.308, A:A.309, A:D.342, A:A.343, D:G.284, D:D.316, D:S.317, D:S.317, D:S.317, D:S.317 NAD.3: 29 residues within 4Å: Chain B: T.104, S.105, N.106, L.107, S.109, T.131, A.132, G.133, E.136, E.137, D.238, G.282, G.283, I.306, N.307, T.308, A.309, A.341, D.342, A.343 Chain C: G.284, V.285, H.288, D.313, S.315, D.316, S.317 Ligands: NAD.5, GC7.6 21 PLIP interactions: 14 interactions with chain B, 7 interactions with chain C Hydrogen bonds: B:T.104, B:S.105, B:S.105, B:N.106, B:S.109, B:T.131, B:A.132, B:G.133, B:G.283, B:T.308, B:T.308, B:D.342, B:D.342, B:A.343, C:G.284, C:D.313, C:D.316, C:S.317, C:S.317, C:S.317, C:S.317 NAD.5: 29 residues within 4Å: Chain B: G.284, V.285, H.288, D.313, S.315, D.316, S.317 Chain C: T.104, S.105, N.106, L.107, S.109, T.131, A.132, G.133, E.136, E.137, D.238, G.282, G.283, I.306, N.307, T.308, A.309, A.341, D.342, A.343 Ligands: NAD.3, GC7.4 20 PLIP interactions: 6 interactions with chain B, 14 interactions with chain C Hydrogen bonds: B:G.284, B:D.316, B:S.317, B:S.317, B:S.317, B:S.317, C:T.104, C:S.105, C:S.105, C:N.106, C:S.109, C:T.131, C:A.132, C:G.133, C:G.283, C:T.308, C:A.309, C:D.342, C:D.342, C:A.343 NAD.7: 29 residues within 4Å: Chain A: 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, D.238, G.282, G.283, I.306, N.307, T.308, A.309, A.341, D.342, A.343 Ligands: NAD.1, GC7.2 17 PLIP interactions: 11 interactions with chain D, 6 interactions with chain A Hydrogen bonds: D:S.105, D:S.105, D:N.106, D:S.109, D:A.132, D:G.133, D:D.238, D:G.283, D:T.308, D:D.342, D:A.343, A:G.284, A:D.316, A:S.317, A:S.317, A:S.317, A:S.317

4 x GC7: 1-GUANIDINIUM-7-AMINOHEPTANE(Non-covalent)

GC7.2: 16 residues within 4Å: Chain A: H.288, N.292, L.295, G.314, S.315, D.316, A.319, E.323, W.327, K.329 Chain D: N.106, I.166, G.167, S.240, D.243 Ligands: NAD.7 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:W.327, A:W.327, A:W.327 Hydrogen bonds: A:N.292, A:N.292, A:G.314, A:S.315, D:G.167 Salt bridges: A:D.316, A:E.323 GC7.4: 16 residues within 4Å: Chain B: H.288, N.292, L.295, G.314, S.315, D.316, A.319, E.323, W.327, K.329 Chain C: I.166, G.167, G.239, S.240, D.243 Ligands: NAD.5 10 PLIP interactions: 2 interactions with chain C, 8 interactions with chain B Hydrogen bonds: C:R.165, C:G.167, B:N.292, B:N.292, B:G.314 Hydrophobic interactions: B:W.327, B:W.327, B:W.327 Salt bridges: B:D.316, B:E.323 GC7.6: 16 residues within 4Å: Chain B: N.106, I.166, G.167, S.240, D.243 Chain C: H.288, N.292, L.295, G.314, S.315, D.316, A.319, E.323, W.327, K.329 Ligands: NAD.3 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:W.327, C:W.327, C:W.327 Hydrogen bonds: C:N.292, C:N.292, C:G.314, C:S.315, B:G.167 Salt bridges: C:D.316, C:E.323 GC7.8: 16 residues within 4Å: Chain A: I.166, G.167, G.239, S.240, D.243 Chain D: H.288, N.292, L.295, G.314, S.315, D.316, A.319, E.323, W.327, K.329 Ligands: NAD.1 10 PLIP interactions: 8 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:W.327, D:W.327, D:W.327 Hydrogen bonds: D:N.292, D:N.292, D:G.314, A:R.165, A:G.167 Salt bridges: D:D.316, D:E.323

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Umland, T.C. et al., A New Crystal Structure of Deoxyhypusine Synthase Reveals the Configuration of the Active Enzyme and of an Enzyme-NAD-Inhibitor Ternary Complex. J.Biol.Chem. (2004)

Release Date

2004-07-13

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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