SMTL ID : 4m8n.1 (1 other biounit)

Crystal Structure of PlexinC1/Rap1B Complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.29 Å

Oligo State

hetero-2-2-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain C: S.20, T.38, D.60, T.61 Ligands: GDP.2, AF3.3 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:S.20, C:T.38 MG.4: 7 residues within 4Å: Chain D: K.19, S.20, T.38, D.60, T.61 Ligands: GDP.5, AF3.6 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:S.20, D:T.38, D:D.60

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

GDP.2: 21 residues within 4Å: Chain A: R.163 Chain C: G.16, V.17, G.18, K.19, S.20, A.21, F.31, E.33, K.34, Y.35, T.38, N.119, K.120, D.122, L.123, S.150, A.151, K.152 Ligands: MG.1, AF3.3 22 PLIP interactions: 20 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:G.16, C:V.17, C:G.18, C:K.19, C:S.20, C:A.21, C:K.34, C:K.34, C:D.36, C:T.38, C:N.119, C:K.120, C:K.120, C:S.150, C:A.151, C:K.152 Salt bridges: C:K.19, C:D.122, A:R.163, A:R.163 pi-Stacking: C:F.31, C:F.31 GDP.5: 21 residues within 4Å: Chain B: L.160, R.163 Chain D: G.16, V.17, G.18, K.19, S.20, A.21, F.31, E.33, K.34, Y.35, T.38, N.119, K.120, D.122, S.150, A.151, K.152 Ligands: MG.4, AF3.6 18 PLIP interactions: 17 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:G.16, D:V.17, D:G.18, D:K.19, D:S.20, D:A.21, D:K.34, D:K.34, D:D.36, D:N.119, D:K.120, D:K.120, D:S.150, D:A.151, D:K.152, B:R.163 Salt bridges: D:K.19, D:D.122

2 x AF3: ALUMINUM FLUORIDE(Non-covalent)

AF3.3: 13 residues within 4Å: Chain A: R.163 Chain C: S.14, G.15, G.16, K.19, S.20, P.37, T.38, A.62, G.63, Q.66 Ligands: MG.1, GDP.2 No protein-ligand interaction detected (PLIP) AF3.6: 13 residues within 4Å: Chain B: R.163 Chain D: G.15, G.16, K.19, S.20, P.37, T.38, T.61, A.62, G.63, Q.66 Ligands: MG.4, GDP.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y. et al., Structural basis for activation and non-canonical catalysis of the Rap GTPase activating protein domain of plexin. Elife (2013)

Release Date

2013-10-09

Peptides

PlexinC1 Intracellular Region: AB
Ras-related protein Rap-1b: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
E

D
H

PlexinC1 Intracellular Region

Ras-related protein Rap-1b

Related Entries With Identical Sequence