SMTL ID : 2j9c.1

Structure of GlnK1 with bound effectors indicates regulatory mechanism for ammonia uptake

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-trimer

Ligands

3 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 25 residues within 4Å: Chain A: I.9, G.37, R.38, G.39, V.40, E.46, K.60, P.88, G.89, D.90, G.91, K.92, F.94 Chain C: G.29, M.30, T.31, E.64, L.65, V.66, R.103, R.105, A.113, L.114, H.117 Ligands: MG.2 24 PLIP interactions: 11 interactions with chain C, 13 interactions with chain A Hydrogen bonds: C:T.31, C:V.66, C:V.66, A:G.39, A:V.40, A:V.40, A:G.89, A:G.91 Water bridges: C:G.29, C:V.104, C:R.105, C:H.117, A:E.46, A:E.46, A:K.60, A:K.60, A:D.90 Salt bridges: C:R.103, C:R.103, C:R.105, C:H.117, A:K.92, A:K.92 pi-Stacking: A:F.94 ATP.8: 25 residues within 4Å: Chain A: G.29, M.30, T.31, E.64, L.65, V.66, R.103, R.105, L.114, H.117 Chain B: I.9, G.37, R.38, G.39, V.40, E.46, K.60, P.88, G.89, D.90, G.91, K.92, F.94 Ligands: MG.9, CL.10 21 PLIP interactions: 12 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:V.40, B:G.89, B:G.91, A:V.66, A:V.66 Water bridges: B:G.39, B:G.39, B:E.46, B:K.60, B:D.90, B:D.90, A:G.29, A:R.105, A:H.117 Salt bridges: B:K.92, B:K.92, A:R.103, A:R.103, A:R.105, A:H.117 pi-Stacking: B:F.94 ATP.13: 25 residues within 4Å: Chain B: G.29, M.30, T.31, E.64, L.65, V.66, R.103, R.105, A.113, L.114, H.117 Chain C: I.9, G.37, R.38, G.39, V.40, E.46, K.60, P.88, G.89, D.90, G.91, K.92, F.94 Ligands: MG.14 20 PLIP interactions: 13 interactions with chain C, 7 interactions with chain B Hydrogen bonds: C:V.40, C:G.89, C:G.91, B:V.66, B:V.66 Water bridges: C:G.39, C:G.39, C:G.39, C:G.39, C:E.46, C:K.60, C:D.90, B:V.104 Salt bridges: C:K.92, C:K.92, B:R.103, B:R.103, B:R.105, B:H.117 pi-Stacking: C:F.94

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: G.89 Ligands: ATP.1 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain B: G.89 Ligands: ATP.8 No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Chain C: G.89 Ligands: ATP.13 No protein-ligand interaction detected (PLIP)

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 6 residues within 4Å: Chain A: K.5, I.96 Chain B: K.5, I.96 Chain C: K.5, I.96 Ligand excluded by PLIP CL.4: 1 residues within 4Å: Chain A: K.20 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain A: A.113, L.114 Chain B: V.40, K.92 Ligands: ATP.8 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain A: V.72, D.73 Chain C: R.100 Ligand excluded by PLIP

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

EDO.5: 3 residues within 4Å: Chain A: Q.41 Chain C: S.23, V.28 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:S.23 Water bridges: A:Q.41, A:I.54 EDO.11: 4 residues within 4Å: Chain B: R.105, T.106 Chain C: R.84, G.86 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Water bridges: C:R.84, C:G.86, B:T.106 Hydrogen bonds: B:R.105 EDO.12: 1 residues within 4Å: Chain B: K.107 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.107 EDO.16: 7 residues within 4Å: Chain C: P.12, E.34, V.35, K.36, P.59, K.60, V.61 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.34, C:K.60, C:K.60

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

ACT.6: 9 residues within 4Å: Chain A: S.33, E.34, V.35 Chain B: S.33, E.34, V.35 Chain C: S.33, E.34 Ligands: ACT.7 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Water bridges: A:E.34, C:E.34 ACT.7: 8 residues within 4Å: Chain A: S.33, K.62 Chain B: S.33, V.35, K.62 Chain C: S.33, K.62 Ligands: ACT.6 9 PLIP interactions: 5 interactions with chain B, 2 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: B:V.35, B:K.62 Hydrogen bonds: B:S.33, B:S.33, C:S.33, A:S.33 Salt bridges: B:K.62, C:K.62, A:K.62 ACT.17: 3 residues within 4Å: Chain C: K.36, Y.53, P.59 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:P.59 Hydrogen bonds: C:Y.53 Salt bridges: C:K.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yildiz, O. et al., Structure of Glnk1 with Bound Effectors Indicates Regulatory Mechanism for Ammonia Uptake. Embo J. (2007)

Release Date

2007-01-16

Peptides

HYPOTHETICAL NITROGEN REGULATORY PII-LIKE PROTEIN MJ0059: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

HYPOTHETICAL NITROGEN REGULATORY PII-LIKE PROTEIN MJ0059

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