SMTL ID : 1nvu.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-8-4-mer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: S.17, T.35 Ligands: GTP.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.17, A:T.35, H2O.1, H2O.1 MG.8: 3 residues within 4Å: Chain D: S.17, T.35 Ligands: GTP.10 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:S.17, D:T.35, H2O.20, H2O.20 MG.15: 3 residues within 4Å: Chain G: S.17, T.35 Ligands: GTP.17 4 PLIP interactions: 2 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:S.17, G:T.35, H2O.40, H2O.40 MG.22: 3 residues within 4Å: Chain J: S.17, T.35 Ligands: GTP.24 4 PLIP interactions: 2 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:S.17, J:T.35, H2O.60, H2O.60

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

PO4.2: 4 residues within 4Å: Chain A: E.153, D.154, Y.157, R.161 Ligand excluded by PLIP PO4.4: 11 residues within 4Å: Chain B: A.11, G.12, G.13, V.14, G.15, K.16, S.17, G.59, E.62 Chain C: L.373, E.377 Ligand excluded by PLIP PO4.5: 5 residues within 4Å: Chain C: V.59, R.60, H.130, H.134, H.135 Ligand excluded by PLIP PO4.6: 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 PO4.7: 1 residues within 4Å: Chain C: R.95 Ligand excluded by PLIP PO4.9: 4 residues within 4Å: Chain D: E.153, D.154, Y.157, R.161 Ligand excluded by PLIP PO4.11: 11 residues within 4Å: Chain E: A.11, G.12, G.13, V.14, G.15, K.16, S.17, G.59, E.62 Chain F: L.373, E.377 Ligand excluded by PLIP PO4.12: 5 residues within 4Å: Chain F: V.59, R.60, H.130, H.134, H.135 Ligand excluded by PLIP PO4.13: 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 PO4.14: 1 residues within 4Å: Chain F: R.95 Ligand excluded by PLIP PO4.16: 4 residues within 4Å: Chain G: E.153, D.154, Y.157, R.161 Ligand excluded by PLIP PO4.18: 11 residues within 4Å: Chain H: A.11, G.12, G.13, V.14, G.15, K.16, S.17, G.59, E.62 Chain I: L.373, E.377 Ligand excluded by PLIP PO4.19: 5 residues within 4Å: Chain I: V.59, R.60, H.130, H.134, H.135 Ligand excluded by PLIP PO4.20: 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 PO4.21: 1 residues within 4Å: Chain I: R.95 Ligand excluded by PLIP PO4.23: 4 residues within 4Å: Chain J: E.153, D.154, Y.157, R.161 Ligand excluded by PLIP PO4.25: 11 residues within 4Å: Chain K: A.11, G.12, G.13, V.14, G.15, K.16, S.17, G.59, E.62 Chain L: L.373, E.377 Ligand excluded by PLIP PO4.26: 5 residues within 4Å: Chain L: V.59, R.60, H.130, H.134, H.135 Ligand excluded by PLIP PO4.27: 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 PO4.28: 1 residues within 4Å: Chain L: R.95 Ligand excluded by PLIP

4 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.3: 26 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, G.59, G.60, E.62, 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:S.17, A:A.18, A:V.29, A:Y.32, A:T.35, A:G.60, A:E.62, A:N.116, A:K.117, A:K.117, A:A.146, A:K.147 Water bridges: A:S.17, A:S.17, A:S.17, A:T.35 Salt bridges: A:K.16, A:K.16, A:D.119 pi-Stacking: A:F.28, A:F.28 GTP.10: 26 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, G.59, G.60, E.62, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.8 25 PLIP interactions: 25 interactions with chain D Hydrogen bonds: D:G.13, D:V.14, D:G.15, D:K.16, D:S.17, D:A.18, D:V.29, D:Y.32, D:T.35, D:G.60, D:E.62, D:N.116, D:K.117, D:K.117, D:A.146, D:K.147 Water bridges: D:S.17, D:S.17, D:S.17, D:T.35 Salt bridges: D:K.16, D:K.16, D:D.119 pi-Stacking: D:F.28, D:F.28 GTP.17: 26 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, G.59, G.60, E.62, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.15 25 PLIP interactions: 25 interactions with chain G Hydrogen bonds: G:G.13, G:V.14, G:G.15, G:K.16, G:S.17, G:A.18, G:V.29, G:Y.32, G:T.35, G:G.60, G:E.62, G:N.116, G:K.117, G:K.117, G:A.146, G:K.147 Water bridges: G:S.17, G:S.17, G:S.17, G:T.35 Salt bridges: G:K.16, G:K.16, G:D.119 pi-Stacking: G:F.28, G:F.28 GTP.24: 26 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, G.59, G.60, E.62, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.22 25 PLIP interactions: 25 interactions with chain J Hydrogen bonds: J:G.13, J:V.14, J:G.15, J:K.16, J:S.17, J:A.18, J:V.29, J:Y.32, J:T.35, J:G.60, J:E.62, J:N.116, J:K.117, J:K.117, J:A.146, J:K.147 Water bridges: J:S.17, J:S.17, J:S.17, J:T.35 Salt bridges: J:K.16, J:K.16, J:D.119 pi-Stacking: J:F.28, J: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: ABDEGHJK
Son of sevenless protein homolog 1: CFIL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
Q

B
R

D
Q

E
R

G
Q

H
R

J
Q

K
R

C
S

F
S

I
S

L
S

Transforming protein p21/H-RAS-1

Son of sevenless protein homolog 1

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