SMTL ID : 1tu4.7 (9 other biounits)

Crystal Structure of Rab5-GDP Complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

6 x CO: COBALT (II) ION(Non-covalent)

CO.1: 2 residues within 4Å: Chain A: S.21 Ligands: GDP.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.21, H2O.1, H2O.1, H2O.1 CO.3: 3 residues within 4Å: Chain B: S.21, D.62 Ligands: GDP.7 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.21, H2O.5, H2O.5, H2O.5, H2O.5 CO.4: 4 residues within 4Å: Chain A: Y.69, H.70 Chain B: E.67, H.70 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:E.67, B:H.70, A:H.70, H2O.2, H2O.6 CO.8: 2 residues within 4Å: Chain C: S.21 Ligands: GDP.9 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:S.21, H2O.8, H2O.8, H2O.8 CO.10: 3 residues within 4Å: Chain D: S.21, D.62 Ligands: GDP.14 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:S.21, H2O.13, H2O.13, H2O.13, H2O.13 CO.11: 4 residues within 4Å: Chain C: Y.69, H.70 Chain D: E.67, H.70 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: D:E.67, D:H.70, C:H.70, H2O.10, H2O.14

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

GDP.2: 15 residues within 4Å: Chain A: E.15, A.17, V.18, G.19, K.20, S.21, S.22, N.120, K.121, D.123, L.124, S.150, A.151, K.152 Ligands: CO.1 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:E.15, A:A.17, A:V.18, A:G.19, A:K.20, A:S.21, A:S.22, A:S.22, A:E.67, A:N.120, A:K.121, A:K.121, A:S.150, A:A.151, A:K.152 Water bridges: A:K.20, A:K.152 Salt bridges: A:K.20, A:D.123 GDP.7: 21 residues within 4Å: Chain B: E.15, S.16, A.17, V.18, G.19, K.20, S.21, S.22, N.120, K.121, D.123, L.124, S.150, A.151, K.152 Chain C: Q.106, R.107, A.109, S.110, P.111 Ligands: CO.3 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:A.17, B:V.18, B:G.19, B:K.20, B:S.21, B:S.22, B:S.22, B:N.120, B:K.121, B:K.121, B:S.150, B:A.151, B:K.152, C:R.107, C:A.109 Salt bridges: B:D.123 GDP.9: 15 residues within 4Å: Chain C: E.15, A.17, V.18, G.19, K.20, S.21, S.22, N.120, K.121, D.123, L.124, S.150, A.151, K.152 Ligands: CO.8 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:E.15, C:A.17, C:V.18, C:G.19, C:K.20, C:S.21, C:S.22, C:S.22, C:E.67, C:N.120, C:K.121, C:K.121, C:S.150, C:A.151, C:K.152 Water bridges: C:K.20, C:K.152 Salt bridges: C:K.20, C:D.123 GDP.14: 21 residues within 4Å: Chain A: Q.106, R.107, A.109, S.110, P.111 Chain D: E.15, S.16, A.17, V.18, G.19, K.20, S.21, S.22, N.120, K.121, D.123, L.124, S.150, A.151, K.152 Ligands: CO.10 16 PLIP interactions: 14 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:A.17, D:V.18, D:G.19, D:K.20, D:S.21, D:S.22, D:S.22, D:N.120, D:K.121, D:K.121, D:S.150, D:A.151, D:K.152, A:R.107, A:A.109 Salt bridges: D:D.123

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

SO4.5: 3 residues within 4Å: Chain B: Q.66, E.67, R.68 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.68 Water bridges: B:E.67, B:E.67 Salt bridges: B:R.68 SO4.6: 3 residues within 4Å: Chain B: A.64, G.65, Q.66 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.65, B:Q.66, B:Q.66 SO4.12: 3 residues within 4Å: Chain D: Q.66, E.67, R.68 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.68 Water bridges: D:E.67, D:E.67 Salt bridges: D:R.68 SO4.13: 3 residues within 4Å: Chain D: A.64, G.65, Q.66 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.65, D:Q.66, D:Q.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, G. et al., Structural basis of Rab5-Rabaptin5 interaction in endocytosis. Nat.Struct.Mol.Biol. (2004)

Release Date

2004-10-05

Peptides

Ras-related protein Rab-5A: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Ras-related protein Rab-5A

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