SMTL ID : 5kho.1

Rasip1 RA domain in complex with Rap1B

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.78 Å

Oligo State

hetero-2-2-mer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: D.77, R.98, V.109, W.113, R.121 Chain B: D.77, R.98, V.109, W.113 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.77, B:D.77, B:R.98, A:R.98, A:R.98, A:R.121

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain C: S.17, T.35 Ligands: GNP.3 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.17, C:T.35, H2O.1, H2O.1 MG.4: 3 residues within 4Å: Chain D: S.17, T.35 Ligands: GNP.5 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:S.17, D:T.35, H2O.1, H2O.1

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

GNP.3: 26 residues within 4Å: Chain C: S.11, G.12, G.13, V.14, G.15, K.16, S.17, A.18, F.28, V.29, E.30, K.31, Y.32, P.34, T.35, T.58, A.59, G.60, N.116, K.117, D.119, L.120, S.147, A.148, K.149 Ligands: MG.2 23 PLIP interactions: 23 interactions with chain C Hydrogen bonds: C:G.13, C:V.14, C:G.15, C:K.16, C:K.16, C:S.17, C:A.18, C:V.29, C:T.35, C:T.35, C:T.58, C:G.60, C:N.116, C:K.117, C:K.117, C:A.148, C:K.149 Water bridges: C:S.17, C:S.17 Salt bridges: C:D.119 pi-Stacking: C:F.28, C:F.28 pi-Cation interactions: C:K.117 GNP.5: 26 residues within 4Å: Chain D: S.11, G.12, G.13, V.14, G.15, K.16, S.17, A.18, F.28, V.29, E.30, K.31, Y.32, P.34, T.35, T.58, A.59, G.60, N.116, K.117, D.119, L.120, S.147, A.148, K.149 Ligands: MG.4 27 PLIP interactions: 27 interactions with chain D Hydrogen bonds: D:G.13, D:V.14, D:G.15, D:K.16, D:K.16, D:K.16, D:S.17, D:A.18, D:V.29, D:Y.32, D:Y.32, D:T.35, D:T.58, D:G.60, D:N.116, D:K.117, D:S.147, D:A.148, D:K.149 Water bridges: D:S.17, D:S.17, D:T.35, D:T.35 Salt bridges: D:D.119 pi-Stacking: D:F.28, D:F.28 pi-Cation interactions: D:K.117

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gingras, A.R. et al., Structural Basis of Dimeric Rasip1 RA Domain Recognition of the Ras Subfamily of GTP-Binding Proteins. Structure (2016)

Release Date

2016-10-19

Peptides

Ras-interacting protein 1: AB
Ras-related protein Rap-1b: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Ras-interacting protein 1

Ras-related protein Rap-1b

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