SMTL ID : 1nvw.2 (2 other biounits)

Structural evidence for feedback activation by RasGTP of the Ras-specific nucleotide exchange factor SOS

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-16-8-mer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: S.17, T.35, D.57, T.58 Ligands: GNP.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.17, A:T.35, H2O.1 MG.10: 5 residues within 4Å: Chain D: S.17, T.35, D.57, T.58 Ligands: GNP.13 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:S.17, D:T.35, H2O.3 MG.19: 5 residues within 4Å: Chain G: S.17, T.35, D.57, T.58 Ligands: GNP.22 3 PLIP interactions: 2 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:S.17, G:T.35, H2O.5 MG.28: 5 residues within 4Å: Chain J: S.17, T.35, D.57, T.58 Ligands: GNP.31 3 PLIP interactions: 2 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:S.17, J:T.35, H2O.7 MG.37: 5 residues within 4Å: Chain M: S.17, T.35, D.57, T.58 Ligands: GNP.40 3 PLIP interactions: 2 interactions with chain M, 1 Ligand-Water interactions Metal complexes: M:S.17, M:T.35, H2O.9 MG.46: 5 residues within 4Å: Chain P: S.17, T.35, D.57, T.58 Ligands: GNP.49 3 PLIP interactions: 2 interactions with chain P, 1 Ligand-Water interactions Metal complexes: P:S.17, P:T.35, H2O.11 MG.55: 5 residues within 4Å: Chain S: S.17, T.35, D.57, T.58 Ligands: GNP.58 3 PLIP interactions: 2 interactions with chain S, 1 Ligand-Water interactions Metal complexes: S:S.17, S:T.35, H2O.13 MG.64: 5 residues within 4Å: Chain V: S.17, T.35, D.57, T.58 Ligands: GNP.67 3 PLIP interactions: 2 interactions with chain V, 1 Ligand-Water interactions Metal complexes: V:S.17, V:T.35, H2O.15

56 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 6 residues within 4Å: Chain A: D.38, S.39, Y.40 Chain C: H.130, H.134 Ligands: PO4.6 Ligand excluded by PLIP PO4.3: 4 residues within 4Å: Chain A: E.153, D.154, Y.157, R.161 Ligand excluded by PLIP PO4.5: 9 residues within 4Å: Chain B: G.13, V.14, G.15, K.16, S.17, A.59, E.62 Chain C: L.373, E.377 Ligand excluded by PLIP PO4.6: 6 residues within 4Å: Chain C: V.59, R.60, H.130, H.134, H.135 Ligands: PO4.2 Ligand excluded by PLIP PO4.7: 7 residues within 4Å: Chain B: E.63 Chain C: K.249, E.250, R.261 Chain H: S.127, R.128, Q.131 Ligand excluded by PLIP PO4.8: 6 residues within 4Å: Chain C: R.95 Chain O: Y.144, R.148, E.151 Chain U: R.385, H.386 Ligand excluded by PLIP PO4.9: 6 residues within 4Å: Chain C: E.18, I.22, F.23, E.25 Chain U: E.92, A.93 Ligand excluded by PLIP PO4.11: 6 residues within 4Å: Chain D: D.38, S.39, Y.40 Chain F: H.130, H.134 Ligands: PO4.15 Ligand excluded by PLIP PO4.12: 4 residues within 4Å: Chain D: E.153, D.154, Y.157, R.161 Ligand excluded by PLIP PO4.14: 9 residues within 4Å: Chain E: G.13, V.14, G.15, K.16, S.17, A.59, E.62 Chain F: L.373, E.377 Ligand excluded by PLIP PO4.15: 6 residues within 4Å: Chain F: V.59, R.60, H.130, H.134, H.135 Ligands: PO4.11 Ligand excluded by PLIP PO4.16: 7 residues within 4Å: Chain E: E.63 Chain F: K.249, E.250, R.261 Chain K: S.127, R.128, Q.131 Ligand excluded by PLIP PO4.17: 6 residues within 4Å: Chain F: R.95 Chain R: Y.144, R.148, E.151 Chain X: R.385, H.386 Ligand excluded by PLIP PO4.18: 6 residues within 4Å: Chain F: E.18, I.22, F.23, E.25 Chain X: E.92, A.93 Ligand excluded by PLIP PO4.20: 6 residues within 4Å: Chain G: D.38, S.39, Y.40 Chain I: H.130, H.134 Ligands: PO4.24 Ligand excluded by PLIP PO4.21: 4 residues within 4Å: Chain G: E.153, D.154, Y.157, R.161 Ligand excluded by PLIP PO4.23: 9 residues within 4Å: Chain H: G.13, V.14, G.15, K.16, S.17, A.59, E.62 Chain I: L.373, E.377 Ligand excluded by PLIP PO4.24: 6 residues within 4Å: Chain I: V.59, R.60, H.130, H.134, H.135 Ligands: PO4.20 Ligand excluded by PLIP PO4.25: 7 residues within 4Å: Chain E: S.127, R.128, Q.131 Chain H: E.63 Chain I: K.249, E.250, R.261 Ligand excluded by PLIP PO4.26: 6 residues within 4Å: Chain I: R.95 Chain O: R.385, H.386 Chain X: Y.144, R.148, E.151 Ligand excluded by PLIP PO4.27: 6 residues within 4Å: Chain I: E.18, I.22, F.23, E.25 Chain O: E.92, A.93 Ligand excluded by PLIP PO4.29: 6 residues within 4Å: Chain J: D.38, S.39, Y.40 Chain L: H.130, H.134 Ligands: PO4.33 Ligand excluded by PLIP PO4.30: 4 residues within 4Å: Chain J: E.153, D.154, Y.157, R.161 Ligand excluded by PLIP PO4.32: 9 residues within 4Å: Chain K: G.13, V.14, G.15, K.16, S.17, A.59, E.62 Chain L: L.373, E.377 Ligand excluded by PLIP PO4.33: 6 residues within 4Å: Chain L: V.59, R.60, H.130, H.134, H.135 Ligands: PO4.29 Ligand excluded by PLIP PO4.34: 7 residues within 4Å: Chain B: S.127, R.128, Q.131 Chain K: E.63 Chain L: K.249, E.250, R.261 Ligand excluded by PLIP PO4.35: 6 residues within 4Å: Chain L: R.95 Chain R: R.385, H.386 Chain U: Y.144, R.148, E.151 Ligand excluded by PLIP PO4.36: 6 residues within 4Å: Chain L: E.18, I.22, F.23, E.25 Chain R: E.92, A.93 Ligand excluded by PLIP PO4.38: 6 residues within 4Å: Chain M: D.38, S.39, Y.40 Chain O: H.130, H.134 Ligands: PO4.42 Ligand excluded by PLIP PO4.39: 4 residues within 4Å: Chain M: E.153, D.154, Y.157, R.161 Ligand excluded by PLIP PO4.41: 9 residues within 4Å: Chain N: G.13, V.14, G.15, K.16, S.17, A.59, E.62 Chain O: L.373, E.377 Ligand excluded by PLIP PO4.42: 6 residues within 4Å: Chain O: V.59, R.60, H.130, H.134, H.135 Ligands: PO4.38 Ligand excluded by PLIP PO4.43: 7 residues within 4Å: Chain N: E.63 Chain O: K.249, E.250, R.261 Chain T: S.127, R.128, Q.131 Ligand excluded by PLIP PO4.44: 6 residues within 4Å: Chain C: Y.144, R.148, E.151 Chain I: R.385, H.386 Chain O: R.95 Ligand excluded by PLIP PO4.45: 6 residues within 4Å: Chain I: E.92, A.93 Chain O: E.18, I.22, F.23, E.25 Ligand excluded by PLIP PO4.47: 6 residues within 4Å: Chain P: D.38, S.39, Y.40 Chain R: H.130, H.134 Ligands: PO4.51 Ligand excluded by PLIP PO4.48: 4 residues within 4Å: Chain P: E.153, D.154, Y.157, R.161 Ligand excluded by PLIP PO4.50: 9 residues within 4Å: Chain Q: G.13, V.14, G.15, K.16, S.17, A.59, E.62 Chain R: L.373, E.377 Ligand excluded by PLIP PO4.51: 6 residues within 4Å: Chain R: V.59, R.60, H.130, H.134, H.135 Ligands: PO4.47 Ligand excluded by PLIP PO4.52: 7 residues within 4Å: Chain Q: E.63 Chain R: K.249, E.250, R.261 Chain W: S.127, R.128, Q.131 Ligand excluded by PLIP PO4.53: 6 residues within 4Å: Chain F: Y.144, R.148, E.151 Chain L: R.385, H.386 Chain R: R.95 Ligand excluded by PLIP PO4.54: 6 residues within 4Å: Chain L: E.92, A.93 Chain R: E.18, I.22, F.23, E.25 Ligand excluded by PLIP PO4.56: 6 residues within 4Å: Chain S: D.38, S.39, Y.40 Chain U: H.130, H.134 Ligands: PO4.60 Ligand excluded by PLIP PO4.57: 4 residues within 4Å: Chain S: E.153, D.154, Y.157, R.161 Ligand excluded by PLIP PO4.59: 9 residues within 4Å: Chain T: G.13, V.14, G.15, K.16, S.17, A.59, E.62 Chain U: L.373, E.377 Ligand excluded by PLIP PO4.60: 6 residues within 4Å: Chain U: V.59, R.60, H.130, H.134, H.135 Ligands: PO4.56 Ligand excluded by PLIP PO4.61: 7 residues within 4Å: Chain Q: S.127, R.128, Q.131 Chain T: E.63 Chain U: K.249, E.250, R.261 Ligand excluded by PLIP PO4.62: 6 residues within 4Å: Chain C: R.385, H.386 Chain L: Y.144, R.148, E.151 Chain U: R.95 Ligand excluded by PLIP PO4.63: 6 residues within 4Å: Chain C: E.92, A.93 Chain U: E.18, I.22, F.23, E.25 Ligand excluded by PLIP PO4.65: 6 residues within 4Å: Chain V: D.38, S.39, Y.40 Chain X: H.130, H.134 Ligands: PO4.69 Ligand excluded by PLIP PO4.66: 4 residues within 4Å: Chain V: E.153, D.154, Y.157, R.161 Ligand excluded by PLIP PO4.68: 9 residues within 4Å: Chain W: G.13, V.14, G.15, K.16, S.17, A.59, E.62 Chain X: L.373, E.377 Ligand excluded by PLIP PO4.69: 6 residues within 4Å: Chain X: V.59, R.60, H.130, H.134, H.135 Ligands: PO4.65 Ligand excluded by PLIP PO4.70: 7 residues within 4Å: Chain N: S.127, R.128, Q.131 Chain W: E.63 Chain X: K.249, E.250, R.261 Ligand excluded by PLIP PO4.71: 6 residues within 4Å: Chain F: R.385, H.386 Chain I: Y.144, R.148, E.151 Chain X: R.95 Ligand excluded by PLIP PO4.72: 6 residues within 4Å: Chain F: E.92, A.93 Chain X: E.18, I.22, F.23, E.25 Ligand excluded by PLIP

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

GNP.4: 27 residues within 4Å: Chain A: A.11, G.12, G.13, V.14, G.15, K.16, S.17, A.18, F.28, V.29, D.30, E.31, Y.32, P.34, T.35, T.58, A.59, G.60, Q.61, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.1 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:G.13, A:V.14, A:G.15, A:K.16, A:K.16, A:S.17, A:S.17, A:A.18, A:V.29, A:D.30, A:Y.32, A:Y.32, A:T.35, A:T.58, A:G.60, A:Q.61, A:N.116, A:K.117, A:K.117, A:A.146, A:K.147 Water bridges: A:D.33 Salt bridges: A:D.119 pi-Stacking: A:F.28, A:F.28 GNP.13: 27 residues within 4Å: Chain D: A.11, G.12, G.13, V.14, G.15, K.16, S.17, A.18, F.28, V.29, D.30, E.31, Y.32, P.34, T.35, T.58, A.59, G.60, Q.61, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.10 25 PLIP interactions: 25 interactions with chain D Hydrogen bonds: D:G.13, D:V.14, D:G.15, D:K.16, D:K.16, D:S.17, D:S.17, D:A.18, D:V.29, D:D.30, D:Y.32, D:Y.32, D:T.35, D:T.58, D:G.60, D:Q.61, D:N.116, D:K.117, D:K.117, D:A.146, D:K.147 Water bridges: D:D.33 Salt bridges: D:D.119 pi-Stacking: D:F.28, D:F.28 GNP.22: 27 residues within 4Å: Chain G: A.11, G.12, G.13, V.14, G.15, K.16, S.17, A.18, F.28, V.29, D.30, E.31, Y.32, P.34, T.35, T.58, A.59, G.60, Q.61, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.19 25 PLIP interactions: 25 interactions with chain G Hydrogen bonds: G:G.13, G:V.14, G:G.15, G:K.16, G:K.16, G:S.17, G:S.17, G:A.18, G:V.29, G:D.30, G:Y.32, G:Y.32, G:T.35, G:T.58, G:G.60, G:Q.61, G:N.116, G:K.117, G:K.117, G:A.146, G:K.147 Water bridges: G:D.33 Salt bridges: G:D.119 pi-Stacking: G:F.28, G:F.28 GNP.31: 27 residues within 4Å: Chain J: A.11, G.12, G.13, V.14, G.15, K.16, S.17, A.18, F.28, V.29, D.30, E.31, Y.32, P.34, T.35, T.58, A.59, G.60, Q.61, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.28 25 PLIP interactions: 25 interactions with chain J Hydrogen bonds: J:G.13, J:V.14, J:G.15, J:K.16, J:K.16, J:S.17, J:S.17, J:A.18, J:V.29, J:D.30, J:Y.32, J:Y.32, J:T.35, J:T.58, J:G.60, J:Q.61, J:N.116, J:K.117, J:K.117, J:A.146, J:K.147 Water bridges: J:D.33 Salt bridges: J:D.119 pi-Stacking: J:F.28, J:F.28 GNP.40: 27 residues within 4Å: Chain M: A.11, G.12, G.13, V.14, G.15, K.16, S.17, A.18, F.28, V.29, D.30, E.31, Y.32, P.34, T.35, T.58, A.59, G.60, Q.61, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.37 24 PLIP interactions: 24 interactions with chain M Hydrogen bonds: M:G.13, M:V.14, M:G.15, M:K.16, M:K.16, M:S.17, M:S.17, M:A.18, M:V.29, M:Y.32, M:T.35, M:T.35, M:T.58, M:G.60, M:Q.61, M:N.116, M:K.117, M:K.117, M:A.146, M:K.147 Water bridges: M:D.33 Salt bridges: M:D.119 pi-Stacking: M:F.28, M:F.28 GNP.49: 27 residues within 4Å: Chain P: A.11, G.12, G.13, V.14, G.15, K.16, S.17, A.18, F.28, V.29, D.30, E.31, Y.32, P.34, T.35, T.58, A.59, G.60, Q.61, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.46 24 PLIP interactions: 24 interactions with chain P Hydrogen bonds: P:G.13, P:V.14, P:G.15, P:K.16, P:K.16, P:S.17, P:S.17, P:A.18, P:V.29, P:Y.32, P:T.35, P:T.35, P:T.58, P:G.60, P:Q.61, P:N.116, P:K.117, P:K.117, P:A.146, P:K.147 Water bridges: P:D.33 Salt bridges: P:D.119 pi-Stacking: P:F.28, P:F.28 GNP.58: 27 residues within 4Å: Chain S: A.11, G.12, G.13, V.14, G.15, K.16, S.17, A.18, F.28, V.29, D.30, E.31, Y.32, P.34, T.35, T.58, A.59, G.60, Q.61, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.55 24 PLIP interactions: 24 interactions with chain S Hydrogen bonds: S:G.13, S:V.14, S:G.15, S:K.16, S:K.16, S:S.17, S:S.17, S:A.18, S:V.29, S:Y.32, S:T.35, S:T.35, S:T.58, S:G.60, S:Q.61, S:N.116, S:K.117, S:K.117, S:A.146, S:K.147 Water bridges: S:D.33 Salt bridges: S:D.119 pi-Stacking: S:F.28, S:F.28 GNP.67: 27 residues within 4Å: Chain V: A.11, G.12, G.13, V.14, G.15, K.16, S.17, A.18, F.28, V.29, D.30, E.31, Y.32, P.34, T.35, T.58, A.59, G.60, Q.61, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.64 24 PLIP interactions: 24 interactions with chain V Hydrogen bonds: V:G.13, V:V.14, V:G.15, V:K.16, V:K.16, V:S.17, V:S.17, V:A.18, V:V.29, V:Y.32, V:T.35, V:T.35, V:T.58, V:G.60, V:Q.61, V:N.116, V:K.117, V:K.117, V:A.146, V:K.147 Water bridges: V:D.33 Salt bridges: V:D.119 pi-Stacking: V:F.28, V:F.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Margarit, S.M. et al., Structural evidence for feedback activation by RasGTP of the Ras-specific nucleotide exchange factor SOS. Cell(Cambridge,Mass.) (2003)

Release Date

2003-04-01

Peptides

Transforming protein p21/H-RAS-1: ABDEGHJKMNPQSTVW
Son of sevenless protein homolog 1: CFILORUX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
Q

B
R

D
Q

E
R

G
Q

H
R

J
Q

K
R

M
Q

N
R

P
Q

Q
R

S
Q

T
R

V
Q

W
R

C
S

F
S

I
S

L
S

O
S

R
S

U
S

X
S

Transforming protein p21/H-RAS-1

Son of sevenless protein homolog 1

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