SMTL ID : 7zhf.1

GPN-loop GTPase from Sulfolobus acidocaldarius closed state (GppNHp)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)

GNP.1: 20 residues within 4Å: Chain A: A.29, G.30, S.31, G.32, K.33, T.34, T.35, G.124, K.189, D.191, L.192, S.240, S.241, T.242 Chain B: L.86, G.87, P.88, N.89, S.90 Ligands: MG.2 28 PLIP interactions: 7 interactions with chain B, 21 interactions with chain A Hydrogen bonds: B:G.87, B:N.89, B:S.90, B:S.90, B:S.90, A:G.30, A:S.31, A:G.32, A:K.33, A:K.33, A:T.34, A:T.35, A:T.35, A:G.124, A:K.189, A:K.189, A:S.240, A:S.241, A:T.242, A:T.242 Water bridges: B:E.85, B:N.89, A:T.34, A:T.34, A:T.34, A:T.34, A:S.241 Salt bridges: A:D.191 GNP.5: 20 residues within 4Å: Chain A: L.86, G.87, P.88, N.89, S.90 Chain B: A.29, G.30, S.31, G.32, K.33, T.34, T.35, G.124, K.189, D.191, L.192, S.240, S.241, T.242 Ligands: MG.6 25 PLIP interactions: 18 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:G.30, B:S.31, B:G.32, B:K.33, B:K.33, B:T.34, B:T.35, B:T.35, B:G.124, B:K.189, B:K.189, B:S.240, B:S.241, B:T.242, B:T.242, A:G.87, A:N.89, A:S.90, A:S.90, A:S.90 Water bridges: B:T.34, B:S.241, A:E.85, A:N.89 Salt bridges: B:D.191

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: K.33, T.34 Ligands: GNP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.34, H2O.1, H2O.3, H2O.4 MG.6: 3 residues within 4Å: Chain B: K.33, T.34 Ligands: GNP.5 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.34, H2O.9, H2O.10, H2O.11

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 11 residues within 4Å: Chain A: S.173, S.174, F.177 Chain B: K.163, L.166, S.167, L.170, S.221, L.224, V.225, I.228 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.173, A:S.174, B:K.163 GOL.7: 11 residues within 4Å: Chain A: K.163, L.166, S.167, L.170, S.221, L.224, V.225, I.228 Chain B: S.173, S.174, F.177 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.173, B:S.174, A:K.163

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

CL.4: 5 residues within 4Å: Chain A: D.97, R.132, T.134 Chain B: Y.157, L.158 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain A: Y.157, L.158 Chain B: D.97, R.132, T.134 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Korf, L. et al., Archaeal GPN-loop GTPases involve a lock-switch-rock mechanism for GTP hydrolysis. Mbio (2023)

Release Date

2023-10-25

Peptides

GTPase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

GTPase

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