SMTL ID : 5ovo.1

Structure of DraG-GlnZ-delta42-54 complex from Azospirillum brasilense

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

hetero-3-3-mer

Ligands

6 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 15 residues within 4Å: Chain A: G.99, D.100, T.101, T.102, E.121, Y.122, A.124, G.125, N.126, G.127, H.158, A.211, Y.212 Chain D: R.38 Ligands: MG.3 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:D.100, A:T.101, A:T.101, A:T.102, A:T.102, A:T.102, A:T.102, A:E.121, A:A.124, A:G.125, A:N.126, A:G.127, D:R.38 Water bridges: A:N.126, A:N.160, A:A.211 Salt bridges: A:H.158 pi-Stacking: A:Y.212 ADP.4: 21 residues within 4Å: Chain B: G.27, L.28, T.29, E.49, V.50, A.51, R.88, R.90 Chain D: I.7, G.35, F.36, G.37, R.38, Q.39, K.45, I.73, G.74, D.75, G.76, K.77, F.79 19 PLIP interactions: 12 interactions with chain D, 7 interactions with chain B Hydrogen bonds: D:R.38, D:Q.39, D:G.74, D:D.75, D:K.77, B:T.29, B:A.51, B:A.51 Water bridges: D:G.35, D:G.37, D:K.45, D:K.45, D:G.76, B:I.89, B:R.90 Salt bridges: D:K.77, D:K.77, B:R.88, B:R.90 ADP.6: 15 residues within 4Å: Chain C: G.99, D.100, T.101, T.102, E.121, Y.122, A.124, G.125, N.126, G.127, H.158, A.211, Y.212 Chain F: R.38 Ligands: MG.8 18 PLIP interactions: 17 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:D.100, C:T.101, C:T.101, C:T.102, C:T.102, C:T.102, C:T.102, C:E.121, C:A.124, C:G.125, C:N.126, C:G.127, F:R.38 Water bridges: C:N.126, C:N.160, C:A.211 Salt bridges: C:H.158 pi-Stacking: C:Y.212 ADP.9: 21 residues within 4Å: Chain D: G.27, L.28, T.29, E.49, V.50, A.51, R.88, R.90 Chain F: I.7, G.35, F.36, G.37, R.38, Q.39, K.45, I.73, G.74, D.75, G.76, K.77, F.79 19 PLIP interactions: 7 interactions with chain D, 12 interactions with chain F Hydrogen bonds: D:T.29, D:A.51, D:A.51, F:R.38, F:Q.39, F:G.74, F:D.75, F:K.77 Water bridges: D:I.89, D:R.90, F:G.35, F:G.37, F:K.45, F:K.45, F:G.76 Salt bridges: D:R.88, D:R.90, F:K.77, F:K.77 ADP.11: 15 residues within 4Å: Chain B: R.38 Chain E: G.99, D.100, T.101, T.102, E.121, Y.122, A.124, G.125, N.126, G.127, H.158, A.211, Y.212 Ligands: MG.13 18 PLIP interactions: 17 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:D.100, E:T.101, E:T.101, E:T.102, E:T.102, E:T.102, E:T.102, E:E.121, E:A.124, E:G.125, E:N.126, E:G.127, B:R.38 Water bridges: E:N.126, E:N.160, E:A.211 Salt bridges: E:H.158 pi-Stacking: E:Y.212 ADP.14: 21 residues within 4Å: Chain B: I.7, G.35, F.36, G.37, R.38, Q.39, K.45, I.73, G.74, D.75, G.76, K.77, F.79 Chain F: G.27, L.28, T.29, E.49, V.50, A.51, R.88, R.90 19 PLIP interactions: 7 interactions with chain F, 12 interactions with chain B Hydrogen bonds: F:T.29, F:A.51, F:A.51, B:R.38, B:Q.39, B:G.74, B:D.75, B:K.77 Water bridges: F:I.89, F:R.90, B:G.35, B:G.37, B:K.45, B:K.45, B:G.76 Salt bridges: F:R.88, F:R.90, B:K.77, B:K.77

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: E.28, D.60, D.61, D.243, D.245, T.246 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.245, H2O.1, H2O.2 MG.3: 7 residues within 4Å: Chain A: T.101, Y.122, H.123, A.124, G.125, H.158 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:Y.122 MG.7: 6 residues within 4Å: Chain C: E.28, D.60, D.61, D.243, D.245, T.246 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.245, H2O.21, H2O.21 MG.8: 7 residues within 4Å: Chain C: T.101, Y.122, H.123, A.124, G.125, H.158 Ligands: ADP.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:Y.122 MG.12: 6 residues within 4Å: Chain E: E.28, D.60, D.61, D.243, D.245, T.246 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.245, H2O.40, H2O.41 MG.13: 7 residues within 4Å: Chain E: T.101, Y.122, H.123, A.124, G.125, H.158 Ligands: ADP.11 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:Y.122

3 x MN: MANGANESE (II) ION(Non-covalent)

MN.5: 4 residues within 4Å: Chain A: R.103, R.107 Chain B: Q.26, G.27 No protein-ligand interaction detected (PLIP) MN.10: 4 residues within 4Å: Chain C: R.103, R.107 Chain D: Q.26, G.27 No protein-ligand interaction detected (PLIP) MN.15: 4 residues within 4Å: Chain E: R.103, R.107 Chain F: Q.26, G.27 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Berthold, C.L. et al., Structure of DraG-GlnZ-delta42-54 complex from Azospirillum brasilense. To Be Published

Release Date

2017-10-11

Peptides

ADP-ribosyl-(Dinitrogen reductase) hydrolase: ACE
Nitrogen regulatory protein P-II 1: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

ADP-ribosyl-(Dinitrogen reductase) hydrolase

Nitrogen regulatory protein P-II 1

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