SMTL ID : 4lv8.1 (2 other biounits)

Murine IRGa6 bound to Toxoplasma ROP5C, a pseudokinase GDI

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

hetero-1-1-mer

Ligands

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

ADP.1: 19 residues within 4Å: Chain A: R.71, G.73, D.74, R.75, S.76, V.78, A.91, K.93, L.134, M.167, P.168, A.169, A.170, D.173, D.223, N.224, F.226 Ligands: MG.2, EDO.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:D.74, A:D.74, A:R.75, A:S.76, A:P.168, A:A.170, A:D.223, A:N.224 Water bridges: A:V.72, A:K.93 Salt bridges: A:K.93, A:K.93

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.223 Ligands: ADP.1 No protein-ligand interaction detected (PLIP)

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

EDO.3: 6 residues within 4Å: Chain A: L.134, M.167, F.226, G.236, D.237 Ligands: ADP.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.134, A:D.237 Water bridges: A:K.93, A:D.237 EDO.4: 5 residues within 4Å: Chain A: E.88, D.89, F.90, S.137, P.168 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.88, A:S.137, A:S.137 Water bridges: A:D.89 EDO.5: 4 residues within 4Å: Chain A: R.247, A.265, S.266, T.267 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.247, A:S.266, A:S.266, A:T.267 EDO.6: 6 residues within 4Å: Chain A: R.26, A.29, L.30, L.70, R.71, V.72 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.71, A:V.72, A:V.72 EDO.7: 8 residues within 4Å: Chain A: A.207, L.210, Q.211, H.272, D.275, A.276, L.346, P.347 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.207, A:Q.211, A:H.272, A:D.275, A:A.276 EDO.8: 8 residues within 4Å: Chain A: Y.185, L.187, F.193 Chain B: T.168, R.169, F.170, R.192, N.222 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.192, B:R.192, A:L.187 Water bridges: B:F.170 EDO.9: 8 residues within 4Å: Chain A: R.188, S.189, T.190, F.193 Chain B: N.222, N.225, T.226, E.229 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:T.190, B:N.222, B:N.225, B:E.229 EDO.11: 4 residues within 4Å: Chain B: M.56, T.64, D.300, L.301 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.64, B:D.300, B:L.301 EDO.12: 6 residues within 4Å: Chain B: E.202, K.206, T.209, D.211, K.214, V.215 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.206, B:K.206, B:D.211, B:D.211 Water bridges: B:E.202, B:T.209, A:R.188 EDO.13: 5 residues within 4Å: Chain B: T.168, K.194, S.197, D.198, N.201 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.194, B:D.198, B:N.201 Water bridges: B:T.168, A:F.183

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.10: 14 residues within 4Å: Chain B: E.87, T.88, G.89, S.90, G.91, K.92, S.93, S.94, T.112, K.194, D.196, S.241, N.242, K.243 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:G.89, B:S.90, B:G.91, B:K.92, B:S.93, B:S.93, B:S.94, B:S.94, B:T.112, B:K.194, B:K.194, B:S.241, B:N.242, B:N.242, B:K.243 Water bridges: B:N.104, B:T.112, B:E.116, B:D.136, B:S.197 Salt bridges: B:D.196

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Reese, M.L. et al., Murine IRGa6 bound to Toxoplasma ROP5C, a pseudokinase GDI. To be Published

Release Date

2013-09-25

Peptides

Rhoptry protein 5 C: A
Interferon-inducible GTPase 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Rhoptry protein 5 C

Interferon-inducible GTPase 1

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