SMTL ID : 2c2h.1 (1 other biounit)

CRYSTAL STRUCTURE OF THE HUMAN RAC3 IN COMPLEX WITH GDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

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

GDP.1: 16 residues within 4Å: Chain A: D.11, G.12, A.13, V.14, G.15, K.16, T.17, C.18, F.28, K.116, D.118, L.119, S.158, A.159, L.160 Ligands: MG.13 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:D.11, A:A.13, A:V.14, A:G.15, A:K.16, A:T.17, A:C.18, A:K.116, A:A.159, A:L.160 Water bridges: A:K.16, A:K.16, A:T.17, A:L.19, A:Q.61, A:K.116, A:K.116 Salt bridges: A:K.16, A:D.118 pi-Stacking: A:F.28 GDP.2: 9 residues within 4Å: Chain A: P.99, E.100, H.103, H.104 Ligands: GDP.3, CA.6, CA.7, MG.14, MG.15 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.99, A:P.99 Salt bridges: A:H.103 pi-Stacking: A:H.103, A:H.103 GDP.3: 11 residues within 4Å: Chain A: H.103, H.104, P.106 Ligands: GDP.2, GDP.4, CA.6, CA.7, CA.8, SO4.11, MG.14, MG.15 4 PLIP interactions: 4 interactions with chain A Water bridges: A:H.104 Salt bridges: A:H.103, A:H.104, A:H.104 GDP.4: 8 residues within 4Å: Chain A: P.106, H.107 Ligands: GDP.3, CA.8, CA.9, CA.10, SO4.11, SO4.12 5 PLIP interactions: 5 interactions with chain A Water bridges: A:Q.74, A:Q.74, A:Q.74 Salt bridges: A:H.107 pi-Stacking: A:H.107 GDP.5: 5 residues within 4Å: Chain A: L.117, R.120, Y.139, E.156, R.163 8 PLIP interactions: 8 interactions with chain A Water bridges: A:R.120, A:Y.139, A:E.156, A:E.156 Salt bridges: A:R.120, A:R.163 pi-Stacking: A:Y.139 pi-Cation interactions: A:Y.139

6 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.6: 3 residues within 4Å: Chain A: H.104 Ligands: GDP.2, GDP.3 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.104, H2O.2 CA.7: 3 residues within 4Å: Chain A: H.103 Ligands: GDP.2, GDP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.103 CA.8: 4 residues within 4Å: Ligands: GDP.3, GDP.4, CA.10, SO4.11 No protein-ligand interaction detected (PLIP) CA.9: 5 residues within 4Å: Chain A: P.106, H.107 Ligands: GDP.4, SO4.11, SO4.12 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.107 CA.10: 2 residues within 4Å: Ligands: GDP.4, CA.8 No protein-ligand interaction detected (PLIP) CA.16: 2 residues within 4Å: Ligands: SO4.11, SO4.12 No protein-ligand interaction detected (PLIP)

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.11: 8 residues within 4Å: Chain A: P.106, H.107 Ligands: GDP.3, GDP.4, CA.8, CA.9, SO4.12, CA.16 No protein-ligand interaction detected (PLIP) SO4.12: 5 residues within 4Å: Chain A: H.107 Ligands: GDP.4, CA.9, SO4.11, CA.16 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.107

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

MG.13: 3 residues within 4Å: Chain A: T.17, D.57 Ligands: GDP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.17, H2O.1, H2O.1, H2O.4, H2O.4 MG.14: 2 residues within 4Å: Ligands: GDP.2, GDP.3 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Ligands: GDP.2, GDP.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Debreczeni, J.E. et al., Crystal Structure of the Human Rac3 in Complex with Gdp. To be Published

Release Date

2005-10-13

Peptides

RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 3

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