SMTL ID : 3rph.1

Crystal Structure of ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Bacillus subtilis co-crystallized with ATP/Mg2+.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: K.189 Ligands: AMP.2, PO4.3 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain B: K.189 Ligands: AMP.6, PO4.7 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain C: K.189 Ligands: AMP.10, PO4.11 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain D: K.189 Ligands: AMP.14, PO4.15 No protein-ligand interaction detected (PLIP)

8 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 19 residues within 4Å: Chain A: H.152, K.189, G.190, N.191, T.193, G.208, N.209, G.210, L.212, A.213, T.217, G.218, L.221, H.246 Chain C: A.23, S.25, K.27 Ligands: MG.1, PO4.3 17 PLIP interactions: 10 interactions with chain A, 7 interactions with chain C Hydrogen bonds: A:G.190, A:T.193, A:T.217, A:G.218, C:S.25, C:S.25 Water bridges: A:E.155, A:K.189, A:T.193, A:T.193, A:K.214, C:K.27, C:K.27, C:K.27, C:K.27 Salt bridges: A:K.189, C:K.27 AMP.4: 8 residues within 4Å: Chain A: H.152, P.153, G.154, V.164 Chain C: H.26, K.27, G.28, K.60 9 PLIP interactions: 2 interactions with chain A, 7 interactions with chain C Salt bridges: A:H.152, C:K.27, C:K.60 pi-Stacking: A:H.152, C:H.26, C:H.26 Water bridges: C:S.25, C:H.26, C:K.27 AMP.6: 19 residues within 4Å: Chain B: H.152, K.189, G.190, N.191, T.193, G.208, N.209, G.210, L.212, A.213, T.217, G.218, L.221, H.246 Chain D: A.23, S.25, K.27 Ligands: MG.5, PO4.7 17 PLIP interactions: 10 interactions with chain B, 7 interactions with chain D Hydrogen bonds: B:G.190, B:T.193, B:T.217, B:G.218, D:S.25, D:S.25 Water bridges: B:E.155, B:K.189, B:T.193, B:T.193, B:K.214, D:K.27, D:K.27, D:K.27, D:K.27 Salt bridges: B:K.189, D:K.27 AMP.8: 8 residues within 4Å: Chain B: H.152, P.153, G.154, V.164 Chain D: H.26, K.27, G.28, K.60 9 PLIP interactions: 7 interactions with chain D, 2 interactions with chain B Water bridges: D:S.25, D:H.26, D:K.27 Salt bridges: D:K.27, D:K.60, B:H.152 pi-Stacking: D:H.26, D:H.26, B:H.152 AMP.10: 19 residues within 4Å: Chain B: A.23, S.25, K.27 Chain C: H.152, K.189, G.190, N.191, T.193, G.208, N.209, G.210, L.212, A.213, T.217, G.218, L.221, H.246 Ligands: MG.9, PO4.11 17 PLIP interactions: 7 interactions with chain B, 10 interactions with chain C Hydrogen bonds: B:S.25, B:S.25, C:G.190, C:T.193, C:T.217, C:G.218 Water bridges: B:K.27, B:K.27, B:K.27, B:K.27, C:E.155, C:K.189, C:T.193, C:T.193, C:K.214 Salt bridges: B:K.27, C:K.189 AMP.12: 8 residues within 4Å: Chain B: H.26, K.27, G.28, K.60 Chain C: H.152, P.153, G.154, V.164 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain C Water bridges: B:S.25, B:H.26, B:K.27 Salt bridges: B:K.27, B:K.60, C:H.152 pi-Stacking: B:H.26, B:H.26, C:H.152 AMP.14: 19 residues within 4Å: Chain A: A.23, S.25, K.27 Chain D: H.152, K.189, G.190, N.191, T.193, G.208, N.209, G.210, L.212, A.213, T.217, G.218, L.221, H.246 Ligands: MG.13, PO4.15 17 PLIP interactions: 10 interactions with chain D, 7 interactions with chain A Hydrogen bonds: D:G.190, D:T.193, D:T.217, D:G.218, A:S.25, A:S.25 Water bridges: D:E.155, D:K.189, D:T.193, D:T.193, D:K.214, A:K.27, A:K.27, A:K.27, A:K.27 Salt bridges: D:K.189, A:K.27 AMP.16: 8 residues within 4Å: Chain A: H.26, K.27, G.28, K.60 Chain D: H.152, P.153, G.154, V.164 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain D Water bridges: A:S.25, A:H.26, A:K.27 Salt bridges: A:K.27, A:K.60, D:H.152 pi-Stacking: A:H.26, A:H.26, D:H.152

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 8 residues within 4Å: Chain A: G.215, G.216, T.217, G.218, D.219 Chain C: K.27 Ligands: MG.1, AMP.2 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:G.216, A:G.218, A:D.219 Water bridges: A:G.107, C:K.27 Salt bridges: C:K.27 PO4.7: 8 residues within 4Å: Chain B: G.215, G.216, T.217, G.218, D.219 Chain D: K.27 Ligands: MG.5, AMP.6 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:G.216, B:G.218, B:D.219 Water bridges: B:G.107, D:K.27 Salt bridges: D:K.27 PO4.11: 8 residues within 4Å: Chain B: K.27 Chain C: G.215, G.216, T.217, G.218, D.219 Ligands: MG.9, AMP.10 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain C Water bridges: B:K.27, C:G.107 Salt bridges: B:K.27 Hydrogen bonds: C:G.216, C:G.218, C:D.219 PO4.15: 8 residues within 4Å: Chain A: K.27 Chain D: G.215, G.216, T.217, G.218, D.219 Ligands: MG.13, AMP.14 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:G.216, D:G.218, D:D.219 Water bridges: D:G.107, A:K.27 Salt bridges: A:K.27

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shumilin, I.A. et al., Identification of unknown protein function using metabolite cocktail screening. Structure (2012)

Release Date

2011-07-27

Peptides

ADP/ATP-dependent NAD(P)H-hydrate dehydratase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

ADP/ATP-dependent NAD(P)H-hydrate dehydratase

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