SMTL ID : 1z08.5 (4 other biounits)

GppNHp-Bound Rab21 Q53G mutant GTPase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

MG.1: 2 residues within 4Å: Chain A: T.20 Ligands: GNP.5 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.20, H2O.1, H2O.1, H2O.2 MG.2: 2 residues within 4Å: Chain A: M.167, T.170 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:M.167, A:T.170, H2O.3, H2O.4, H2O.4, H2O.5 MG.3: 2 residues within 4Å: Chain A: E.66 Ligands: GNP.5 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:E.66, H2O.3, H2O.3, H2O.4, H2O.5, H2O.9 MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain B: T.20 Ligands: GNP.8 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.20, H2O.10, H2O.10, H2O.11 MG.7: 2 residues within 4Å: Chain B: E.66 Ligands: GNP.8 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:E.66, H2O.12, H2O.12, H2O.13, H2O.14, H2O.17

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

GNP.5: 23 residues within 4Å: Chain A: E.14, G.15, C.16, V.17, G.18, K.19, T.20, S.21, F.31, N.32, D.33, H.35, A.63, G.64, N.119, K.120, D.122, L.123, S.149, A.150, K.151 Ligands: MG.1, MG.3 27 PLIP interactions: 27 interactions with chain A Hydrogen bonds: A:G.15, A:V.17, A:G.18, A:K.19, A:K.19, A:T.20, A:T.20, A:S.21, A:S.21, A:N.32, A:I.36, A:G.64, A:N.119, A:K.120, A:K.120, A:A.150, A:K.151 Water bridges: A:T.20, A:D.33, A:H.35, A:G.64, A:K.151, A:K.151 Salt bridges: A:H.35, A:D.122 pi-Stacking: A:F.31, A:F.31 GNP.8: 23 residues within 4Å: Chain B: E.14, G.15, C.16, V.17, G.18, K.19, T.20, S.21, F.31, N.32, D.33, H.35, A.63, G.64, N.119, K.120, D.122, L.123, S.149, A.150, K.151 Ligands: MG.6, MG.7 27 PLIP interactions: 27 interactions with chain B Hydrogen bonds: B:G.15, B:V.17, B:G.18, B:K.19, B:K.19, B:T.20, B:T.20, B:S.21, B:S.21, B:N.32, B:I.36, B:G.64, B:N.119, B:K.120, B:K.120, B:A.150, B:K.151 Water bridges: B:T.20, B:D.33, B:H.35, B:G.64, B:K.151, B:K.151 Salt bridges: B:H.35, B:D.122 pi-Stacking: B:F.31, B:F.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Eathiraj, S. et al., Structural basis of family-wide Rab GTPase recognition by rabenosyn-5. Nature (2005)

Release Date

2005-07-26

Peptides

Ras-related protein Rab-21: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
C

Ras-related protein Rab-21

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