SMTL ID : 3con.1

Crystal structure of the human NRAS GTPase bound with GDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

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

MG.1: 2 residues within 4Å: Chain A: S.35 Ligands: GDP.5 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.35, H2O.1, H2O.2, H2O.3, H2O.3 MG.2: 1 residues within 4Å: Chain A: G.66 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:G.66, H2O.2, H2O.2, H2O.2, H2O.2, H2O.3 MG.3: 1 residues within 4Å: Chain A: D.56 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.56, H2O.3, H2O.3, H2O.3, H2O.4 MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.5: 21 residues within 4Å: Chain A: A.29, G.30, G.31, V.32, G.33, K.34, S.35, A.36, F.46, V.47, D.48, E.49, Y.50, N.134, K.135, D.137, L.138, S.163, A.164, K.165 Ligands: MG.1 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:A.29, A:G.31, A:V.32, A:G.33, A:K.34, A:S.35, A:A.36, A:V.47, A:N.134, A:K.135, A:K.135, A:S.163, A:A.164, A:K.165 Water bridges: A:K.34, A:S.35, A:S.35, A:Y.50, A:Y.50 Salt bridges: A:K.34, A:D.137 pi-Stacking: A:F.46, A:F.46

8 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.6: 1 residues within 4Å: Chain A: D.65 No protein-ligand interaction detected (PLIP) UNX.7: 4 residues within 4Å: Chain A: K.23, L.24, D.72, L.74 No protein-ligand interaction detected (PLIP) UNX.8: 4 residues within 4Å: Chain A: V.27, G.28, T.76, Y.114 No protein-ligand interaction detected (PLIP) UNX.9: 5 residues within 4Å: Chain A: G.28, A.29, V.99, S.107, I.111 No protein-ligand interaction detected (PLIP) UNX.10: 3 residues within 4Å: Chain A: R.167, V.170, E.171 No protein-ligand interaction detected (PLIP) UNX.11: 2 residues within 4Å: Chain A: S.105, K.106 No protein-ligand interaction detected (PLIP) UNX.12: 2 residues within 4Å: Chain A: N.112, L.113 No protein-ligand interaction detected (PLIP) UNX.13: 3 residues within 4Å: Chain A: D.172, Y.175, R.179 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nedyalkova, L. et al., Crystal structure of the human NRAS GTPase bound with GDP. To be Published

Release Date

2008-04-08

Peptides

GTPase NRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTPase NRas