SMTL ID : 1tu4.5 (9 other biounits)

Crystal Structure of Rab5-GDP Complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-octamer

Ligands

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

CO.1: 3 residues within 4Å: Chain A: S.21 Chain D: N.3 Ligands: GDP.2 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.21, H2O.1, H2O.1, H2O.1, H2O.11 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 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:S.21, H2O.8, H2O.8, H2O.8, H2O.8 CO.10: 2 residues within 4Å: Chain D: S.21 Ligands: GDP.16 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:S.21, H2O.11, H2O.11, H2O.11, H2O.11 CO.11: 4 residues within 4Å: Chain C: Y.69, H.70 Chain D: E.67, H.70 6 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: C:H.70, D:E.67, D:E.67, D:H.70, H2O.9, H2O.9 CO.17: 3 residues within 4Å: Chain E: S.21 Chain H: N.3 Ligands: GDP.18 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:S.21, H2O.12, H2O.12, H2O.12, H2O.22 CO.19: 3 residues within 4Å: Chain F: S.21, D.62 Ligands: GDP.23 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:S.21, H2O.17, H2O.17, H2O.17, H2O.17 CO.20: 4 residues within 4Å: Chain E: Y.69, H.70 Chain F: E.67, H.70 5 PLIP interactions: 2 interactions with chain F, 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: F:E.67, F:H.70, E:H.70, H2O.14, H2O.18 CO.24: 2 residues within 4Å: Chain G: S.21 Ligands: GDP.25 5 PLIP interactions: 1 interactions with chain G, 4 Ligand-Water interactions Metal complexes: G:S.21, H2O.20, H2O.20, H2O.20, H2O.20 CO.26: 2 residues within 4Å: Chain H: S.21 Ligands: GDP.32 5 PLIP interactions: 1 interactions with chain H, 4 Ligand-Water interactions Metal complexes: H:S.21, H2O.22, H2O.23, H2O.23, H2O.23 CO.27: 4 residues within 4Å: Chain G: Y.69, H.70 Chain H: E.67, H.70 6 PLIP interactions: 3 interactions with chain H, 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: H:E.67, H:E.67, H:H.70, G:H.70, H2O.21, H2O.21

8 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 23 PLIP interactions: 19 interactions with chain A, 4 interactions with chain D 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, D:N.3, D:N.3, D:N.3, D:N.3 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 E: 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 E 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, E:R.107, E:A.109 Salt bridges: B:D.123 GDP.9: 17 residues within 4Å: Chain C: E.15, S.16, A.17, V.18, G.19, K.20, S.21, S.22, E.67, N.120, K.121, D.123, L.124, S.150, A.151, K.152 Ligands: CO.8 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: 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 Salt bridges: C:K.20, C:D.123 GDP.16: 21 residues within 4Å: 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 Chain G: Q.106, R.107, A.109, S.110, P.111 Ligands: CO.10 19 PLIP interactions: 17 interactions with chain D, 2 interactions with chain G Hydrogen bonds: D:E.15, 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:A.151, D:K.152, G:R.107, G:A.109 Water bridges: D:S.21, D:S.21, D:D.62 Salt bridges: D:D.123 GDP.18: 15 residues within 4Å: Chain E: 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.17 23 PLIP interactions: 19 interactions with chain E, 4 interactions with chain H Hydrogen bonds: E:E.15, E:A.17, E:V.18, E:G.19, E:K.20, E:S.21, E:S.22, E:S.22, E:E.67, E:N.120, E:K.121, E:K.121, E:S.150, E:A.151, E:K.152 Water bridges: E:K.20, E:K.152, H:N.3, H:N.3, H:N.3, H:N.3 Salt bridges: E:K.20, E:D.123 GDP.23: 21 residues within 4Å: Chain A: Q.106, R.107, A.109, S.110, P.111 Chain F: 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.19 16 PLIP interactions: 14 interactions with chain F, 2 interactions with chain A Hydrogen bonds: F:A.17, F:V.18, F:G.19, F:K.20, F:S.21, F:S.22, F:S.22, F:N.120, F:K.121, F:K.121, F:S.150, F:A.151, F:K.152, A:R.107, A:A.109 Salt bridges: F:D.123 GDP.25: 17 residues within 4Å: Chain G: E.15, S.16, A.17, V.18, G.19, K.20, S.21, S.22, E.67, N.120, K.121, D.123, L.124, S.150, A.151, K.152 Ligands: CO.24 17 PLIP interactions: 17 interactions with chain G Hydrogen bonds: G:A.17, G:V.18, G:G.19, G:K.20, G:S.21, G:S.22, G:S.22, G:E.67, G:E.67, G:N.120, G:K.121, G:K.121, G:S.150, G:A.151, G:K.152 Salt bridges: G:K.20, G:D.123 GDP.32: 21 residues within 4Å: Chain C: Q.106, R.107, A.109, S.110, P.111 Chain H: 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.26 19 PLIP interactions: 2 interactions with chain C, 17 interactions with chain H Hydrogen bonds: C:R.107, C:A.109, H:E.15, H:A.17, H:V.18, H:G.19, H:K.20, H:S.21, H:S.22, H:S.22, H:N.120, H:K.121, H:K.121, H:A.151, H:K.152 Water bridges: H:S.21, H:S.21, H:D.62 Salt bridges: H:D.123

12 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: A.64, G.65, Q.66 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.65, D:Q.66 SO4.13: 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 SO4.14: 3 residues within 4Å: Chain A: R.68 Chain B: Q.108 Chain D: N.3 6 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A, 2 interactions with chain D Hydrogen bonds: B:Q.108, D:N.3, D:N.3 Water bridges: A:S.16, A:G.65 Salt bridges: A:R.68 SO4.15: 2 residues within 4Å: Chain C: R.68 Chain D: Q.108 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Water bridges: C:A.64 Salt bridges: C:R.68 Hydrogen bonds: D:Q.108 SO4.21: 3 residues within 4Å: Chain F: Q.66, E.67, R.68 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:R.68 Water bridges: F:E.67, F:E.67 Salt bridges: F:R.68 SO4.22: 3 residues within 4Å: Chain F: A.64, G.65, Q.66 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:G.65, F:Q.66, F:Q.66 SO4.28: 3 residues within 4Å: Chain H: A.64, G.65, Q.66 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:G.65, H:Q.66 SO4.29: 3 residues within 4Å: Chain H: Q.66, E.67, R.68 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:R.68 Water bridges: H:E.67, H:E.67 Salt bridges: H:R.68 SO4.30: 3 residues within 4Å: Chain E: R.68 Chain F: Q.108 Chain H: N.3 7 PLIP interactions: 3 interactions with chain E, 3 interactions with chain H, 1 interactions with chain F Water bridges: E:S.16, E:G.65 Salt bridges: E:R.68 Hydrogen bonds: H:N.3, H:N.3, H:N.3, F:Q.108 SO4.31: 2 residues within 4Å: Chain G: R.68 Chain H: Q.108 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain H Water bridges: G:A.64 Salt bridges: G:R.68 Hydrogen bonds: H:Q.108

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: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

Ras-related protein Rab-5A

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