SMTL ID : 1nvv.4 (3 other biounits)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: S.17, T.35, D.57 Ligands: GNP.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.17, A:T.35, H2O.1 MG.8: 4 residues within 4Å: Chain D: S.17, T.35, D.57 Ligands: GNP.10 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:S.17, D:T.35, H2O.13

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

PO4.2: 4 residues within 4Å: Chain A: E.153, D.154, Y.157, R.161 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.153, A:E.153, A:D.154 Salt bridges: A:R.161 PO4.4: 9 residues within 4Å: Chain B: A.11, G.13, V.14, G.15, K.16, S.17, A.59, E.62 Chain C: L.373 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.13, B:V.14, B:G.15, B:K.16, B:S.17, B:E.62 Salt bridges: B:K.16 PO4.5: 4 residues within 4Å: Chain C: R.60, H.130, H.134, H.135 6 PLIP interactions: 6 interactions with chain C Water bridges: C:R.60, C:H.135, C:Q.407 Salt bridges: C:H.130, C:H.134, C:H.135 PO4.6: 4 residues within 4Å: Chain B: E.63 Chain C: K.249, E.250, R.261 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Salt bridges: C:K.249, C:R.261 Hydrogen bonds: B:E.63 PO4.7: 4 residues within 4Å: Chain C: R.95 Chain F: Y.144, R.148, E.151 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain C Hydrogen bonds: F:Y.144 Water bridges: F:R.148, F:R.148 Salt bridges: C:R.95 PO4.9: 4 residues within 4Å: Chain D: E.153, D.154, Y.157, R.161 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.153 Salt bridges: D:R.161 PO4.11: 9 residues within 4Å: Chain E: A.11, G.13, V.14, G.15, K.16, S.17, A.59, E.62 Chain F: L.373 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:G.13, E:V.14, E:G.15, E:K.16, E:S.17, E:E.62, E:E.62 Salt bridges: E:K.16 PO4.12: 4 residues within 4Å: Chain F: R.60, H.130, H.134, H.135 6 PLIP interactions: 6 interactions with chain F Water bridges: F:R.60, F:H.135, F:Q.407 Salt bridges: F:H.130, F:H.134, F:H.135 PO4.13: 4 residues within 4Å: Chain E: E.63 Chain F: K.249, E.250, R.261 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:E.250, E:E.63 Salt bridges: F:K.249, F:R.261 PO4.14: 4 residues within 4Å: Chain C: Y.144, R.148, E.151 Chain F: R.95 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:E.151 Water bridges: C:R.148, C:R.148 Salt bridges: F:R.95

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

GNP.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, A.59, G.60, Q.61, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.1 24 PLIP interactions: 24 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:A.18, A:V.29, A:Y.32, A:T.35, 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, A:T.35, A:T.35 Salt bridges: A:D.119 pi-Stacking: A:F.28, A:F.28 pi-Cation interactions: A:K.117 GNP.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, A.59, G.60, Q.61, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.8 22 PLIP interactions: 22 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:A.18, D:V.29, D:T.35, D:T.35, 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 pi-Cation interactions: D:K.117

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: AD
Transforming protein p21/H-RAS-1: BE
Son of sevenless protein homolog 1: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
Q

D
Q

B
R

E
R

C
S

F
S

Transforming protein p21/H-RAS-1

Transforming protein p21/H-RAS-1

Son of sevenless protein homolog 1

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