SMTL ID : 3rrz.1

H-Ras in 70% glycerol: one of 10 in MSCS set

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

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

GNP.1: 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, A.59, G.60, Q.61, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: GOL.7, MG.9 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: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:S.17, A:S.17, A:T.35, A:T.35, A:K.147 Salt bridges: A:D.119 pi-Stacking: A:F.28, A:F.28

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: S.17, I.21, V.29, D.33, T.35, D.38, Y.40 Ligands: GOL.8 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.17, A:D.33, A:D.33, A:Y.40, A:D.57, A:D.57 GOL.3: 4 residues within 4Å: Chain A: T.2, E.3, Y.4, E.76 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.3, A:E.76 Water bridges: A:E.3, A:E.3 GOL.4: 4 residues within 4Å: Chain A: A.11, G.12, N.86, K.88 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.12, A:G.12, A:Q.61, A:N.86, A:K.88, A:K.88 GOL.5: 7 residues within 4Å: Chain A: L.23, N.26, K.42, V.44, R.149, E.153, Y.157 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.26, A:N.26, A:K.42, A:R.149, A:R.149, A:E.153 GOL.6: 5 residues within 4Å: Chain A: Q.22, N.26, H.27, K.147, R.149 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.22, A:K.147 Water bridges: A:F.28 GOL.7: 4 residues within 4Å: Chain A: N.85, K.117, L.120 Ligands: GNP.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.85, A:K.117, A:K.117 GOL.8: 5 residues within 4Å: Chain A: I.21, Q.25, H.27, V.29 Ligands: GOL.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.25, A:Q.25 Water bridges: A:E.31 GOL.13: 3 residues within 4Å: Chain A: H.94, L.133, Y.137 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.137

2 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.9: 4 residues within 4Å: Chain A: S.17, T.35, D.57 Ligands: GNP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.17, A:T.35, H2O.1, H2O.3 MG.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.10: 2 residues within 4Å: Chain A: F.28, D.30 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:F.28, A:D.30, H2O.9 CA.11: 2 residues within 4Å: Chain A: R.102, D.105 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:R.102, A:D.105

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Buhrman, G. et al., Analysis of Binding Site Hot Spots on the Surface of Ras GTPase. J.Mol.Biol. (2011)

Release Date

2011-09-21

Peptides

GTPase HRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTPase HRas

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