- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.20 Å
- Oligo State
- homo-tetramer
- Ligands
- 6 x CO: COBALT (II) ION(Non-covalent)
- 4 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)
GDP.2: 17 residues within 4Å:- Chain A: 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.1
16 PLIP interactions:16 interactions with chain A- Hydrogen bonds: 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
- Salt bridges: A:K.20, A:D.123
GDP.9: 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:E.15, 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:A.151, B:K.152, C:R.107, C:A.109
- Salt bridges: B:D.123
GDP.11: 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.10
17 PLIP interactions:17 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: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.18: 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.12
19 PLIP interactions:17 interactions with chain D, 2 interactions with chain A- 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, A:R.107, A:A.109
- Water bridges: D:S.21, D:S.21, D:D.62
- Salt bridges: D:D.123
- 8 x SO4: SULFATE ION(Non-functional Binders)
SO4.5: 3 residues within 4Å:- Chain B: A.64, G.65, Q.66
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:G.65, B:Q.66
SO4.6: 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
SO4.7: 1 residues within 4Å:- Chain B: N.3
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:N.3, B:N.3
SO4.8: 2 residues within 4Å:- Chain A: R.68
- Chain B: Q.108
3 PLIP interactions:1 interactions with chain B, 2 interactions with chain A- Hydrogen bonds: B:Q.108
- Water bridges: A:A.64
- Salt bridges: A:R.68
SO4.14: 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
SO4.15: 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
SO4.16: 1 residues within 4Å:- Chain D: N.3
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:N.3, D:N.3, D:N.3
SO4.17: 2 residues within 4Å:- Chain C: R.68
- Chain D: Q.108
3 PLIP interactions:1 interactions with chain D, 2 interactions with chain C- Hydrogen bonds: D:Q.108
- Water bridges: C:A.64
- Salt bridges: C:R.68
- 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
CB
DC
CD
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.20 Å
- Oligo State
- homo-tetramer
- Ligands
- 6 x CO: COBALT (II) ION(Non-covalent)
- 4 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)
- 8 x SO4: SULFATE ION(Non-functional Binders)
- 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
CB
DC
CD
D