SMTL ID : 2cl0.1

CRYSTAL STRUCTURE ANALYSIS OF A FLUORESCENT FORM OF H-RAS P21 IN COMPLEX WITH GppNHp

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-trimer

Ligands

15 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: T.124, Q.129 Chain B: Q.129 Chain C: T.124 Ligands: MG.9, MG.17 No protein-ligand interaction detected (PLIP) MG.2: 2 residues within 4Å: Chain A: S.17 Ligands: GNP.7 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.17, H2O.2, H2O.3, H2O.7 MG.3: 1 residues within 4Å: Chain B: D.132 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.132, H2O.5, H2O.5, H2O.12, H2O.12, H2O.12 MG.4: 2 residues within 4Å: Chain A: E.63 Ligands: GNP.7 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.63, H2O.2, H2O.2, H2O.3, H2O.3 MG.5: 1 residues within 4Å: Chain A: G.138 No protein-ligand interaction detected (PLIP) MG.9: 6 residues within 4Å: Chain A: T.124 Chain B: T.124, Q.129 Chain C: Q.129 Ligands: MG.1, MG.17 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain B: S.17 Ligands: GNP.15 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.17, H2O.8, H2O.10, H2O.13 MG.11: 1 residues within 4Å: Chain C: D.132 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:D.132, H2O.11, H2O.11, H2O.18, H2O.18, H2O.18 MG.12: 2 residues within 4Å: Chain B: E.63 Ligands: GNP.15 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.63, H2O.8, H2O.8, H2O.10, H2O.10 MG.13: 1 residues within 4Å: Chain B: G.138 No protein-ligand interaction detected (PLIP) MG.17: 6 residues within 4Å: Chain A: Q.129 Chain B: T.124 Chain C: T.124, Q.129 Ligands: MG.1, MG.9 No protein-ligand interaction detected (PLIP) MG.18: 2 residues within 4Å: Chain C: S.17 Ligands: GNP.23 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:S.17, H2O.15, H2O.16, H2O.20 MG.19: 1 residues within 4Å: Chain A: D.132 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.132, H2O.5, H2O.5, H2O.5, H2O.18, H2O.18 MG.20: 2 residues within 4Å: Chain C: E.63 Ligands: GNP.23 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:E.63, H2O.15, H2O.15, H2O.16, H2O.16 MG.21: 1 residues within 4Å: Chain C: G.138 No protein-ligand interaction detected (PLIP)

3 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.6: 4 residues within 4Å: Chain A: Q.25, D.38, S.39, Y.40 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.39, A:Y.40 Water bridges: A:Q.25 TRS.14: 4 residues within 4Å: Chain B: Q.25, D.38, S.39, Y.40 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.39, B:Y.40 Water bridges: B:Q.25 TRS.22: 4 residues within 4Å: Chain C: Q.25, D.38, S.39, Y.40 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.39, C:Y.40 Water bridges: C:Q.25

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

GNP.7: 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, C.32, D.33, A.59, G.60, E.63, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.2, MG.4, XY2.8 22 PLIP interactions: 22 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.33, A:G.60, A:N.116, A:K.117, A:K.117, A:A.146, A:K.147 Water bridges: A:S.17, A:G.60, A:E.62 Salt bridges: A:D.119 pi-Stacking: A:F.28, A:F.28 GNP.15: 27 residues within 4Å: Chain B: A.11, G.12, G.13, V.14, G.15, K.16, S.17, A.18, F.28, V.29, D.30, E.31, C.32, D.33, A.59, G.60, E.63, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.10, MG.12, XY2.16 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:G.13, B:V.14, B:G.15, B:K.16, B:K.16, B:S.17, B:S.17, B:A.18, B:V.29, B:D.33, B:G.60, B:N.116, B:K.117, B:K.117, B:A.146, B:K.147 Water bridges: B:S.17, B:G.60, B:E.62 Salt bridges: B:D.119 pi-Stacking: B:F.28, B:F.28 GNP.23: 27 residues within 4Å: Chain C: A.11, G.12, G.13, V.14, G.15, K.16, S.17, A.18, F.28, V.29, D.30, E.31, C.32, D.33, A.59, G.60, E.63, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.18, MG.20, XY2.24 22 PLIP interactions: 22 interactions with chain C Hydrogen bonds: C:G.13, C:V.14, C:G.15, C:K.16, C:K.16, C:S.17, C:S.17, C:A.18, C:V.29, C:D.33, C:G.60, C:N.116, C:K.117, C:K.117, C:A.146, C:K.147 Water bridges: C:S.17, C:G.60, C:E.62 Salt bridges: C:D.119 pi-Stacking: C:F.28, C:F.28

3 x XY2: N,N'-DIMETHYL-N-(ACETYL)-N'-(7-NITROBENZ-2-OXA-1,3-DIAZOL-4-YL)ETHYLENEDIAMINE(Covalent)

XY2.8: 3 residues within 4Å: Chain A: E.31, C.32 Ligands: GNP.7 No protein-ligand interaction detected (PLIP) XY2.16: 3 residues within 4Å: Chain B: E.31, C.32 Ligands: GNP.15 No protein-ligand interaction detected (PLIP) XY2.24: 3 residues within 4Å: Chain C: E.31, C.32 Ligands: GNP.23 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Klink, B.U. et al., A Newly Designed Microspectrofluorometer for Kinetic Studies on Protein Crystals in Combination with X-Ray Diffraction. Biophys.J. (2006)

Release Date

2006-05-31

Peptides

GTPASE HRAS: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

B
X

C
X

GTPASE HRAS

Related Entries With Identical Sequence