SMTL ID : 3q3j.1

Crystal structure of plexin A2 RBD in complex with Rnd1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

hetero-4-4-mer

Ligands

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

UNX.1: 4 residues within 4Å: Chain A: I.72, A.73, R.74 Chain B: W.80 Ligand excluded by PLIP UNX.2: 4 residues within 4Å: Chain A: R.4, Q.5, E.8, Y.9 Ligand excluded by PLIP UNX.5: 6 residues within 4Å: Chain A: H.98, Q.100 Chain B: Y.87, Y.88, D.89, N.90 Ligand excluded by PLIP UNX.6: 7 residues within 4Å: Chain B: T.185, S.186, E.187 Chain H: T.185, S.186, E.187 Ligands: UNX.39 Ligand excluded by PLIP UNX.7: 2 residues within 4Å: Chain B: P.160, S.162 Ligand excluded by PLIP UNX.8: 3 residues within 4Å: Chain B: T.141, E.180, G.181 Ligand excluded by PLIP UNX.9: 3 residues within 4Å: Chain B: K.29, S.78, W.80 Ligand excluded by PLIP UNX.10: 2 residues within 4Å: Chain B: V.36, S.85 Ligand excluded by PLIP UNX.11: 1 residues within 4Å: Chain B: Y.178 Ligand excluded by PLIP UNX.12: 4 residues within 4Å: Chain C: I.72, A.73, R.74 Chain D: W.80 Ligand excluded by PLIP UNX.13: 4 residues within 4Å: Chain C: R.4, Q.5, E.8, Y.9 Ligand excluded by PLIP UNX.16: 6 residues within 4Å: Chain C: H.98, Q.100 Chain D: Y.87, Y.88, D.89, N.90 Ligand excluded by PLIP UNX.17: 7 residues within 4Å: Chain D: T.185, S.186, E.187 Chain F: T.185, S.186, E.187 Ligands: UNX.28 Ligand excluded by PLIP UNX.18: 2 residues within 4Å: Chain D: P.160, S.162 Ligand excluded by PLIP UNX.19: 3 residues within 4Å: Chain D: T.141, E.180, G.181 Ligand excluded by PLIP UNX.20: 3 residues within 4Å: Chain D: K.29, S.78, W.80 Ligand excluded by PLIP UNX.21: 2 residues within 4Å: Chain D: V.36, S.85 Ligand excluded by PLIP UNX.22: 1 residues within 4Å: Chain D: Y.178 Ligand excluded by PLIP UNX.23: 4 residues within 4Å: Chain E: I.72, A.73, R.74 Chain F: W.80 Ligand excluded by PLIP UNX.24: 4 residues within 4Å: Chain E: R.4, Q.5, E.8, Y.9 Ligand excluded by PLIP UNX.27: 6 residues within 4Å: Chain E: H.98, Q.100 Chain F: Y.87, Y.88, D.89, N.90 Ligand excluded by PLIP UNX.28: 7 residues within 4Å: Chain D: T.185, S.186, E.187 Chain F: T.185, S.186, E.187 Ligands: UNX.17 Ligand excluded by PLIP UNX.29: 2 residues within 4Å: Chain F: P.160, S.162 Ligand excluded by PLIP UNX.30: 3 residues within 4Å: Chain F: T.141, E.180, G.181 Ligand excluded by PLIP UNX.31: 3 residues within 4Å: Chain F: K.29, S.78, W.80 Ligand excluded by PLIP UNX.32: 2 residues within 4Å: Chain F: V.36, S.85 Ligand excluded by PLIP UNX.33: 1 residues within 4Å: Chain F: Y.178 Ligand excluded by PLIP UNX.34: 4 residues within 4Å: Chain G: I.72, A.73, R.74 Chain H: W.80 Ligand excluded by PLIP UNX.35: 4 residues within 4Å: Chain G: R.4, Q.5, E.8, Y.9 Ligand excluded by PLIP UNX.38: 6 residues within 4Å: Chain G: H.98, Q.100 Chain H: Y.87, Y.88, D.89, N.90 Ligand excluded by PLIP UNX.39: 7 residues within 4Å: Chain B: T.185, S.186, E.187 Chain H: T.185, S.186, E.187 Ligands: UNX.6 Ligand excluded by PLIP UNX.40: 2 residues within 4Å: Chain H: P.160, S.162 Ligand excluded by PLIP UNX.41: 3 residues within 4Å: Chain H: T.141, E.180, G.181 Ligand excluded by PLIP UNX.42: 3 residues within 4Å: Chain H: K.29, S.78, W.80 Ligand excluded by PLIP UNX.43: 2 residues within 4Å: Chain H: V.36, S.85 Ligand excluded by PLIP UNX.44: 1 residues within 4Å: Chain H: Y.178 Ligand excluded by PLIP

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

GNP.3: 25 residues within 4Å: Chain B: D.35, V.36, Q.37, C.38, G.39, K.40, T.41, A.42, Y.52, P.53, E.54, T.55, Y.56, P.58, T.59, T.82, S.83, G.84, K.140, D.142, L.143, S.182, A.183, F.184 Ligands: MG.4 26 PLIP interactions: 26 interactions with chain B Hydrogen bonds: B:Q.37, B:C.38, B:G.39, B:K.40, B:K.40, B:K.40, B:K.40, B:T.41, B:A.42, B:Y.52, B:E.54, B:T.55, B:Y.56, B:T.59, B:T.59, B:T.82, B:G.84, B:K.140, B:K.140, B:A.183, B:F.184 Water bridges: B:M.43, B:V.57, B:V.57 Salt bridges: B:D.142 pi-Stacking: B:Y.52 GNP.14: 25 residues within 4Å: Chain D: D.35, V.36, Q.37, C.38, G.39, K.40, T.41, A.42, Y.52, P.53, E.54, T.55, Y.56, P.58, T.59, T.82, S.83, G.84, K.140, D.142, L.143, S.182, A.183, F.184 Ligands: MG.15 26 PLIP interactions: 26 interactions with chain D Hydrogen bonds: D:Q.37, D:C.38, D:G.39, D:K.40, D:K.40, D:K.40, D:K.40, D:T.41, D:A.42, D:Y.52, D:E.54, D:T.55, D:Y.56, D:T.59, D:T.59, D:T.82, D:G.84, D:K.140, D:K.140, D:A.183, D:F.184 Water bridges: D:M.43, D:V.57, D:V.57 Salt bridges: D:D.142 pi-Stacking: D:Y.52 GNP.25: 25 residues within 4Å: Chain F: D.35, V.36, Q.37, C.38, G.39, K.40, T.41, A.42, Y.52, P.53, E.54, T.55, Y.56, P.58, T.59, T.82, S.83, G.84, K.140, D.142, L.143, S.182, A.183, F.184 Ligands: MG.26 25 PLIP interactions: 25 interactions with chain F Hydrogen bonds: F:Q.37, F:C.38, F:G.39, F:K.40, F:K.40, F:K.40, F:K.40, F:T.41, F:A.42, F:Y.52, F:E.54, F:T.55, F:T.59, F:T.59, F:T.82, F:G.84, F:K.140, F:K.140, F:A.183, F:F.184 Water bridges: F:M.43, F:V.57, F:V.57 Salt bridges: F:D.142 pi-Stacking: F:Y.52 GNP.36: 25 residues within 4Å: Chain H: D.35, V.36, Q.37, C.38, G.39, K.40, T.41, A.42, Y.52, P.53, E.54, T.55, Y.56, P.58, T.59, T.82, S.83, G.84, K.140, D.142, L.143, S.182, A.183, F.184 Ligands: MG.37 25 PLIP interactions: 25 interactions with chain H Hydrogen bonds: H:Q.37, H:C.38, H:G.39, H:K.40, H:K.40, H:K.40, H:K.40, H:T.41, H:A.42, H:Y.52, H:E.54, H:T.55, H:T.59, H:T.59, H:T.82, H:G.84, H:K.140, H:K.140, H:A.183, H:F.184 Water bridges: H:M.43, H:V.57, H:V.57 Salt bridges: H:D.142 pi-Stacking: H:Y.52

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain B: T.41, T.59, D.81 Ligands: GNP.3 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.41, B:T.59, H2O.1, H2O.2 MG.15: 4 residues within 4Å: Chain D: T.41, T.59, D.81 Ligands: GNP.14 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:T.41, D:T.59, H2O.3, H2O.3 MG.26: 4 residues within 4Å: Chain F: T.41, T.59, D.81 Ligands: GNP.25 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:T.41, F:T.59, H2O.4, H2O.4 MG.37: 4 residues within 4Å: Chain H: T.41, T.59, D.81 Ligands: GNP.36 4 PLIP interactions: 2 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:T.41, H:T.59, H2O.6, H2O.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, H. et al., Crystal structure of plexin A2 RBD in complex with Rnd1. to be published

Release Date

2011-01-12

Peptides

Plexin-A2: ACEG
Rho-related GTP-binding protein Rho6: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

G
A

B
B

D
B

F
B

H
B

Plexin-A2

Rho-related GTP-binding protein Rho6