SMTL ID : 2rex.4 (4 other biounits)

Crystal structure of the effector domain of PLXNB1 bound with Rnd1 GTPase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-4-4-mer

Ligands

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

UNX.1: 4 residues within 4Å: Chain A: G.21, E.22, V.70 Chain F: D.33 Ligand excluded by PLIP UNX.2: 2 residues within 4Å: Chain A: L.74, I.75 Ligand excluded by PLIP UNX.3: 2 residues within 4Å: Chain A: I.36, K.40 Ligand excluded by PLIP UNX.4: 4 residues within 4Å: Chain A: D.80, S.83, V.85, R.90 Ligand excluded by PLIP UNX.8: 3 residues within 4Å: Chain B: T.42, V.43, F.44 Ligand excluded by PLIP UNX.9: 1 residues within 4Å: Chain B: N.46 Ligand excluded by PLIP UNX.10: 7 residues within 4Å: Chain B: M.26, I.120, G.121, C.122, G.164, I.173, I.176 Ligand excluded by PLIP UNX.11: 2 residues within 4Å: Chain B: Q.20 Ligands: GNP.7 Ligand excluded by PLIP UNX.12: 5 residues within 4Å: Chain B: V.29, L.30, D.33, E.170, H.174 Ligand excluded by PLIP UNX.13: 3 residues within 4Å: Chain B: Y.35 Chain E: G.103 Ligands: GNP.7 Ligand excluded by PLIP UNX.14: 1 residues within 4Å: Chain B: Y.71 Ligand excluded by PLIP UNX.15: 1 residues within 4Å: Chain B: C.150 Ligand excluded by PLIP UNX.16: 1 residues within 4Å: Chain B: K.154 Ligand excluded by PLIP UNX.17: 4 residues within 4Å: Chain B: S.169, E.170, K.171 Chain E: Q.24 Ligand excluded by PLIP UNX.18: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.19: 4 residues within 4Å: Chain C: G.21, E.22, V.70 Chain H: D.33 Ligand excluded by PLIP UNX.20: 2 residues within 4Å: Chain C: L.74, I.75 Ligand excluded by PLIP UNX.21: 2 residues within 4Å: Chain C: I.36, K.40 Ligand excluded by PLIP UNX.22: 4 residues within 4Å: Chain C: D.80, S.83, V.85, R.90 Ligand excluded by PLIP UNX.26: 3 residues within 4Å: Chain D: T.42, V.43, F.44 Ligand excluded by PLIP UNX.27: 1 residues within 4Å: Chain D: N.46 Ligand excluded by PLIP UNX.28: 7 residues within 4Å: Chain D: M.26, I.120, G.121, C.122, G.164, I.173, I.176 Ligand excluded by PLIP UNX.29: 2 residues within 4Å: Chain D: Q.20 Ligands: GNP.25 Ligand excluded by PLIP UNX.30: 5 residues within 4Å: Chain D: V.29, L.30, D.33, E.170, H.174 Ligand excluded by PLIP UNX.31: 3 residues within 4Å: Chain D: Y.35 Chain G: G.103 Ligands: GNP.25 Ligand excluded by PLIP UNX.32: 1 residues within 4Å: Chain D: Y.71 Ligand excluded by PLIP UNX.33: 1 residues within 4Å: Chain D: C.150 Ligand excluded by PLIP UNX.34: 1 residues within 4Å: Chain D: K.154 Ligand excluded by PLIP UNX.35: 4 residues within 4Å: Chain D: S.169, E.170, K.171 Chain G: Q.24 Ligand excluded by PLIP UNX.36: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.37: 4 residues within 4Å: Chain B: D.33 Chain E: G.21, E.22, V.70 Ligand excluded by PLIP UNX.38: 2 residues within 4Å: Chain E: L.74, I.75 Ligand excluded by PLIP UNX.39: 2 residues within 4Å: Chain E: I.36, K.40 Ligand excluded by PLIP UNX.40: 5 residues within 4Å: Chain E: D.32, L.95, Q.96, K.99, V.100 Ligand excluded by PLIP UNX.41: 4 residues within 4Å: Chain E: P.27, V.28, K.29, Q.46 Ligand excluded by PLIP UNX.45: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.46: 2 residues within 4Å: Chain F: Q.20 Ligands: GNP.44 Ligand excluded by PLIP UNX.47: 2 residues within 4Å: Chain F: T.42, V.43 Ligand excluded by PLIP UNX.48: 2 residues within 4Å: Chain F: D.33, C.34 Ligand excluded by PLIP UNX.49: 2 residues within 4Å: Chain A: G.103 Chain F: Y.35 Ligand excluded by PLIP UNX.50: 2 residues within 4Å: Chain F: Y.39, P.41 Ligand excluded by PLIP UNX.51: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.52: 3 residues within 4Å: Chain F: N.46, Y.47, T.48 Ligand excluded by PLIP UNX.53: 3 residues within 4Å: Chain F: K.32, N.46, Y.47 Ligand excluded by PLIP UNX.54: 3 residues within 4Å: Chain F: R.127, S.145, Y.146 Ligand excluded by PLIP UNX.55: 4 residues within 4Å: Chain D: D.33 Chain G: G.21, E.22, V.70 Ligand excluded by PLIP UNX.56: 2 residues within 4Å: Chain G: L.74, I.75 Ligand excluded by PLIP UNX.57: 2 residues within 4Å: Chain G: I.36, K.40 Ligand excluded by PLIP UNX.58: 5 residues within 4Å: Chain G: D.32, L.95, Q.96, K.99, V.100 Ligand excluded by PLIP UNX.59: 4 residues within 4Å: Chain G: P.27, V.28, K.29, Q.46 Ligand excluded by PLIP UNX.63: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.64: 2 residues within 4Å: Chain H: Q.20 Ligands: GNP.62 Ligand excluded by PLIP UNX.65: 2 residues within 4Å: Chain H: T.42, V.43 Ligand excluded by PLIP UNX.66: 2 residues within 4Å: Chain H: D.33, C.34 Ligand excluded by PLIP UNX.67: 2 residues within 4Å: Chain C: G.103 Chain H: Y.35 Ligand excluded by PLIP UNX.68: 2 residues within 4Å: Chain H: Y.39, P.41 Ligand excluded by PLIP UNX.69: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.70: 3 residues within 4Å: Chain H: N.46, Y.47, T.48 Ligand excluded by PLIP UNX.71: 3 residues within 4Å: Chain H: K.32, N.46, Y.47 Ligand excluded by PLIP UNX.72: 3 residues within 4Å: Chain H: R.127, S.145, Y.146 Ligand excluded by PLIP

4 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain B: T.24, T.42, D.64 Ligands: GNP.7 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.24, B:T.42, H2O.1, H2O.2 MG.23: 4 residues within 4Å: Chain D: T.24, T.42, D.64 Ligands: GNP.25 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:T.24, D:T.42, H2O.2, H2O.3 MG.42: 4 residues within 4Å: Chain F: T.24, T.42, D.64 Ligands: GNP.44 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:T.24, F:T.42, H2O.4, H2O.5 MG.60: 4 residues within 4Å: Chain H: T.24, T.42, D.64 Ligands: GNP.62 4 PLIP interactions: 2 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:T.24, H:T.42, H2O.5, H2O.6

4 x CA: CALCIUM ION(Non-covalent)

CA.6: 3 residues within 4Å: Chain B: Y.35, E.37 Chain E: E.22 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:Y.35, B:E.37, H2O.1, H2O.1, H2O.1 CA.24: 3 residues within 4Å: Chain D: Y.35, E.37 Chain G: E.22 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:Y.35, D:E.37, H2O.2, H2O.2, H2O.2 CA.43: 3 residues within 4Å: Chain A: E.22 Chain F: Y.35, E.37 5 PLIP interactions: 2 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:Y.35, F:E.37, H2O.4, H2O.4, H2O.4 CA.61: 3 residues within 4Å: Chain C: E.22 Chain H: Y.35, E.37 5 PLIP interactions: 2 interactions with chain H, 3 Ligand-Water interactions Metal complexes: H:Y.35, H:E.37, H2O.6, H2O.6, H2O.6

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

GNP.7: 27 residues within 4Å: Chain B: D.18, V.19, Q.20, C.21, G.22, K.23, T.24, A.25, Y.35, P.36, E.37, T.38, Y.39, P.41, T.42, T.65, S.66, G.67, K.123, D.125, L.126, S.165, A.166, F.167 Ligands: MG.5, UNX.11, UNX.13 26 PLIP interactions: 26 interactions with chain B Hydrogen bonds: B:Q.20, B:C.21, B:G.22, B:K.23, B:K.23, B:K.23, B:K.23, B:T.24, B:A.25, B:Y.35, B:E.37, B:T.38, B:Y.39, B:T.42, B:T.65, B:G.67, B:K.123, B:K.123, B:A.166, B:F.167 Water bridges: B:V.40, B:V.40, B:T.42, B:T.42 Salt bridges: B:D.125 pi-Stacking: B:Y.35 GNP.25: 27 residues within 4Å: Chain D: D.18, V.19, Q.20, C.21, G.22, K.23, T.24, A.25, Y.35, P.36, E.37, T.38, Y.39, P.41, T.42, T.65, S.66, G.67, K.123, D.125, L.126, S.165, A.166, F.167 Ligands: MG.23, UNX.29, UNX.31 24 PLIP interactions: 24 interactions with chain D Hydrogen bonds: D:Q.20, D:C.21, D:G.22, D:K.23, D:K.23, D:K.23, D:K.23, D:T.24, D:A.25, D:Y.35, D:E.37, D:T.38, D:T.42, D:T.42, D:T.65, D:G.67, D:K.123, D:K.123, D:A.166, D:F.167 Water bridges: D:V.40, D:V.40 Salt bridges: D:D.125 pi-Stacking: D:Y.35 GNP.44: 25 residues within 4Å: Chain F: D.18, V.19, Q.20, C.21, G.22, K.23, T.24, A.25, Y.35, P.36, E.37, T.38, Y.39, T.42, T.65, S.66, G.67, K.123, D.125, L.126, S.165, A.166, F.167 Ligands: MG.42, UNX.46 26 PLIP interactions: 26 interactions with chain F Hydrogen bonds: F:Q.20, F:C.21, F:G.22, F:K.23, F:K.23, F:K.23, F:T.24, F:A.25, F:Y.35, F:E.37, F:T.38, F:Y.39, F:T.42, F:G.67, F:K.123, F:K.123, F:A.166, F:F.167 Water bridges: F:Y.39, F:V.40, F:V.40, F:T.42, F:T.42, F:T.42 Salt bridges: F:D.125 pi-Stacking: F:Y.35 GNP.62: 25 residues within 4Å: Chain H: D.18, V.19, Q.20, C.21, G.22, K.23, T.24, A.25, Y.35, P.36, E.37, T.38, Y.39, T.42, T.65, S.66, G.67, K.123, D.125, L.126, S.165, A.166, F.167 Ligands: MG.60, UNX.64 24 PLIP interactions: 24 interactions with chain H Hydrogen bonds: H:Q.20, H:C.21, H:G.22, H:K.23, H:K.23, H:K.23, H:T.24, H:A.25, H:Y.35, H:E.37, H:T.38, H:T.42, H:T.42, H:G.67, H:K.123, H:K.123, H:A.166, H:F.167 Water bridges: H:Y.39, H:V.40, H:V.40, H:T.42 Salt bridges: H:D.125 pi-Stacking: H:Y.35

Links

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Citation

Tong, Y. et al., Crystal structure of the effector domain of PLXNB1 bound with Rnd1 GTPase. To be Published

Release Date

2007-11-20

Peptides

Plexin-B1: ACEG
Rho-related GTP-binding protein Rho6: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
C

G
C

B
B

D
B

F
D

H
D

Plexin-B1

Rho-related GTP-binding protein Rho6

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