SMTL ID : 3llu.1

Crystal structure of the nucleotide-binding domain of Ras-related GTP-binding protein C

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-tetramer

Ligands

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

GNP.1: 23 residues within 4Å: Chain A: L.28, R.29, R.30, S.31, G.32, K.33, S.34, S.35, T.49, L.50, L.52, S.54, T.55, P.77, G.78, Q.106, H.137, K.138, D.140, S.178, I.179, Y.180 Ligands: MG.2 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:R.29, A:R.30, A:S.31, A:G.32, A:K.33, A:K.33, A:K.33, A:S.34, A:S.35, A:S.35, A:T.49, A:T.55, A:T.55, A:G.78, A:Q.106, A:K.138, A:I.179 Water bridges: A:S.34, A:S.34, A:K.138, A:K.138 Salt bridges: A:D.140 GNP.12: 23 residues within 4Å: Chain B: L.28, R.29, R.30, S.31, G.32, K.33, S.34, S.35, T.49, L.50, L.52, S.54, T.55, P.77, G.78, Q.106, H.137, K.138, D.140, S.178, I.179, Y.180 Ligands: MG.13 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:R.29, B:R.30, B:S.31, B:G.32, B:K.33, B:K.33, B:K.33, B:S.34, B:S.35, B:S.35, B:T.49, B:T.55, B:T.55, B:G.78, B:Q.106, B:K.138, B:I.179 Water bridges: B:S.34, B:S.34, B:K.138, B:K.138 Salt bridges: B:D.140 GNP.23: 23 residues within 4Å: Chain C: L.28, R.29, R.30, S.31, G.32, K.33, S.34, S.35, T.49, L.50, L.52, S.54, T.55, P.77, G.78, Q.106, H.137, K.138, D.140, S.178, I.179, Y.180 Ligands: MG.24 22 PLIP interactions: 22 interactions with chain C Hydrogen bonds: C:R.29, C:R.30, C:S.31, C:G.32, C:K.33, C:K.33, C:K.33, C:S.34, C:S.35, C:S.35, C:T.49, C:T.55, C:T.55, C:G.78, C:Q.106, C:K.138, C:I.179 Water bridges: C:S.34, C:S.34, C:K.138, C:K.138 Salt bridges: C:D.140 GNP.34: 23 residues within 4Å: Chain D: L.28, R.29, R.30, S.31, G.32, K.33, S.34, S.35, T.49, L.50, L.52, S.54, T.55, P.77, G.78, Q.106, H.137, K.138, D.140, S.178, I.179, Y.180 Ligands: MG.35 22 PLIP interactions: 22 interactions with chain D Hydrogen bonds: D:R.29, D:R.30, D:S.31, D:G.32, D:K.33, D:K.33, D:K.33, D:S.34, D:S.35, D:S.35, D:T.49, D:T.55, D:T.55, D:G.78, D:Q.106, D:K.138, D:I.179 Water bridges: D:S.34, D:S.34, D:K.138, D:K.138 Salt bridges: D:D.140

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: S.34, T.55 Ligands: GNP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.34, A:T.55, H2O.2, H2O.2 MG.13: 3 residues within 4Å: Chain B: S.34, T.55 Ligands: GNP.12 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.34, B:T.55, H2O.5, H2O.5 MG.24: 3 residues within 4Å: Chain C: S.34, T.55 Ligands: GNP.23 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.34, C:T.55, H2O.8, H2O.8 MG.35: 3 residues within 4Å: Chain D: S.34, T.55 Ligands: GNP.34 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:S.34, D:T.55, H2O.12, H2O.12

36 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.3: 1 residues within 4Å: Chain A: H.155 Ligand excluded by PLIP UNX.4: 1 residues within 4Å: Chain A: H.155 Ligand excluded by PLIP UNX.5: 5 residues within 4Å: Chain A: G.27, L.28, Q.79, Y.101, R.115 Ligand excluded by PLIP UNX.6: 3 residues within 4Å: Chain A: E.53, S.54 Chain C: I.196 Ligand excluded by PLIP UNX.7: 2 residues within 4Å: Chain A: S.34, T.55 Ligand excluded by PLIP UNX.8: 1 residues within 4Å: Chain A: R.157 Ligand excluded by PLIP UNX.9: 2 residues within 4Å: Chain A: S.173, F.174 Ligand excluded by PLIP UNX.10: 1 residues within 4Å: Chain A: R.157 Ligand excluded by PLIP UNX.11: 1 residues within 4Å: Chain A: E.111 Ligand excluded by PLIP UNX.14: 1 residues within 4Å: Chain B: H.155 Ligand excluded by PLIP UNX.15: 1 residues within 4Å: Chain B: H.155 Ligand excluded by PLIP UNX.16: 5 residues within 4Å: Chain B: G.27, L.28, Q.79, Y.101, R.115 Ligand excluded by PLIP UNX.17: 3 residues within 4Å: Chain B: E.53, S.54 Chain D: I.196 Ligand excluded by PLIP UNX.18: 2 residues within 4Å: Chain B: S.34, T.55 Ligand excluded by PLIP UNX.19: 1 residues within 4Å: Chain B: R.157 Ligand excluded by PLIP UNX.20: 2 residues within 4Å: Chain B: S.173, F.174 Ligand excluded by PLIP UNX.21: 1 residues within 4Å: Chain B: R.157 Ligand excluded by PLIP UNX.22: 1 residues within 4Å: Chain B: E.111 Ligand excluded by PLIP UNX.25: 1 residues within 4Å: Chain C: H.155 Ligand excluded by PLIP UNX.26: 1 residues within 4Å: Chain C: H.155 Ligand excluded by PLIP UNX.27: 5 residues within 4Å: Chain C: G.27, L.28, Q.79, Y.101, R.115 Ligand excluded by PLIP UNX.28: 3 residues within 4Å: Chain B: I.196 Chain C: E.53, S.54 Ligand excluded by PLIP UNX.29: 2 residues within 4Å: Chain C: S.34, T.55 Ligand excluded by PLIP UNX.30: 1 residues within 4Å: Chain C: R.157 Ligand excluded by PLIP UNX.31: 2 residues within 4Å: Chain C: S.173, F.174 Ligand excluded by PLIP UNX.32: 1 residues within 4Å: Chain C: R.157 Ligand excluded by PLIP UNX.33: 1 residues within 4Å: Chain C: E.111 Ligand excluded by PLIP UNX.36: 1 residues within 4Å: Chain D: H.155 Ligand excluded by PLIP UNX.37: 1 residues within 4Å: Chain D: H.155 Ligand excluded by PLIP UNX.38: 5 residues within 4Å: Chain D: G.27, L.28, Q.79, Y.101, R.115 Ligand excluded by PLIP UNX.39: 3 residues within 4Å: Chain A: I.196 Chain D: E.53, S.54 Ligand excluded by PLIP UNX.40: 2 residues within 4Å: Chain D: S.34, T.55 Ligand excluded by PLIP UNX.41: 1 residues within 4Å: Chain D: R.157 Ligand excluded by PLIP UNX.42: 2 residues within 4Å: Chain D: S.173, F.174 Ligand excluded by PLIP UNX.43: 1 residues within 4Å: Chain D: R.157 Ligand excluded by PLIP UNX.44: 1 residues within 4Å: Chain D: E.111 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nedyalkova, L. et al., Crystal structure of the nucleotide-binding domain of Ras-related GTP-binding protein C. to be published

Release Date

2010-02-09

Peptides

Ras-related GTP-binding protein C: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Ras-related GTP-binding protein C