SMTL ID : 4fmb.4 (3 other biounits)

VirA-Rab1 complex structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-oligomer

Ligands

6 x AF3: ALUMINUM FLUORIDE(Non-covalent)

AF3.1: 11 residues within 4Å: Chain A: R.149, Q.241 Chain B: S.15, G.16, K.19, S.37, T.38, T.62, G.64 Ligands: GDP.2, MG.3 No protein-ligand interaction detected (PLIP) AF3.4: 12 residues within 4Å: Chain C: R.149, Q.241 Chain D: S.15, G.16, K.19, S.37, T.38, T.62, A.63, G.64 Ligands: GDP.5, MG.6 No protein-ligand interaction detected (PLIP) AF3.7: 11 residues within 4Å: Chain E: R.149, Q.241 Chain F: S.15, G.16, K.19, S.37, T.38, T.62, G.64 Ligands: GDP.8, MG.9 No protein-ligand interaction detected (PLIP) AF3.10: 11 residues within 4Å: Chain G: R.149, Q.241 Chain H: S.15, G.16, K.19, S.37, T.38, T.62, G.64 Ligands: GDP.11, MG.12 No protein-ligand interaction detected (PLIP) AF3.13: 12 residues within 4Å: Chain I: R.149, Q.241 Chain J: S.15, G.16, K.19, S.37, T.38, T.62, A.63, G.64 Ligands: GDP.14, MG.15 No protein-ligand interaction detected (PLIP) AF3.16: 11 residues within 4Å: Chain K: R.149, Q.241 Chain L: S.15, G.16, K.19, S.37, T.38, T.62, G.64 Ligands: GDP.17, MG.18 No protein-ligand interaction detected (PLIP)

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

GDP.2: 19 residues within 4Å: Chain A: R.149, R.152 Chain B: D.14, G.16, V.17, G.18, K.19, S.20, C.21, Y.31, N.119, K.120, D.122, L.123, S.149, A.150, K.151 Ligands: AF3.1, MG.3 20 PLIP interactions: 15 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:G.16, B:V.17, B:G.18, B:K.19, B:S.20, B:C.21, B:N.119, B:K.120, B:K.151, A:R.152, A:R.152 Water bridges: B:S.20, B:S.20, B:T.62, B:G.64, A:R.149 Salt bridges: B:K.19, B:D.122, A:R.149, A:R.149 GDP.5: 21 residues within 4Å: Chain C: R.149, R.152 Chain D: D.14, S.15, G.16, V.17, G.18, K.19, S.20, C.21, Y.31, E.33, N.119, K.120, D.122, L.123, S.149, A.150, K.151 Ligands: AF3.4, MG.6 25 PLIP interactions: 5 interactions with chain C, 20 interactions with chain D Hydrogen bonds: C:R.152, C:R.152, D:G.16, D:V.17, D:G.18, D:K.19, D:S.20, D:C.21, D:Y.31, D:E.33, D:E.33, D:N.119, D:K.120, D:K.120, D:A.150, D:K.151 Water bridges: C:R.149, D:S.20, D:S.20, D:T.62, D:G.64 Salt bridges: C:R.149, C:R.149, D:K.19, D:D.122 GDP.8: 21 residues within 4Å: Chain E: R.149, R.152 Chain F: D.14, S.15, G.16, V.17, G.18, K.19, S.20, C.21, Y.31, E.33, N.119, K.120, D.122, L.123, S.149, A.150, K.151 Ligands: AF3.7, MG.9 24 PLIP interactions: 19 interactions with chain F, 5 interactions with chain E Hydrogen bonds: F:G.16, F:V.17, F:G.18, F:K.19, F:S.20, F:C.21, F:Y.31, F:E.33, F:N.119, F:K.120, F:K.120, F:A.150, F:K.151, E:R.152, E:R.152 Water bridges: F:S.20, F:T.38, F:D.61, F:G.64, E:R.149 Salt bridges: F:K.19, F:D.122, E:R.149, E:R.149 GDP.11: 19 residues within 4Å: Chain G: R.149, R.152 Chain H: D.14, G.16, V.17, G.18, K.19, S.20, C.21, Y.31, N.119, K.120, D.122, L.123, S.149, A.150, K.151 Ligands: AF3.10, MG.12 21 PLIP interactions: 16 interactions with chain H, 5 interactions with chain G Hydrogen bonds: H:G.16, H:V.17, H:G.18, H:K.19, H:S.20, H:C.21, H:Y.31, H:N.119, H:K.120, H:K.151, G:R.152, G:R.152 Water bridges: H:S.20, H:S.20, H:T.38, H:G.64, G:R.149 Salt bridges: H:K.19, H:D.122, G:R.149, G:R.149 GDP.14: 21 residues within 4Å: Chain I: R.149, R.152 Chain J: D.14, S.15, G.16, V.17, G.18, K.19, S.20, C.21, Y.31, E.33, N.119, K.120, D.122, L.123, S.149, A.150, K.151 Ligands: AF3.13, MG.15 24 PLIP interactions: 19 interactions with chain J, 5 interactions with chain I Hydrogen bonds: J:G.16, J:V.17, J:G.18, J:K.19, J:S.20, J:C.21, J:E.33, J:N.119, J:K.120, J:K.120, J:D.122, J:A.150, J:K.151, I:R.152, I:R.152 Water bridges: J:S.20, J:S.20, J:D.61, J:G.64, I:R.149 Salt bridges: J:K.19, J:D.122, I:R.149, I:R.149 GDP.17: 21 residues within 4Å: Chain K: R.149, R.152 Chain L: D.14, S.15, G.16, V.17, G.18, K.19, S.20, C.21, Y.31, E.33, N.119, K.120, D.122, L.123, S.149, A.150, K.151 Ligands: AF3.16, MG.18 24 PLIP interactions: 19 interactions with chain L, 5 interactions with chain K Hydrogen bonds: L:G.16, L:V.17, L:G.18, L:K.19, L:S.20, L:C.21, L:E.33, L:E.33, L:N.119, L:K.120, L:K.120, L:A.150, L:K.151, K:R.152, K:R.152 Water bridges: L:S.20, L:S.20, L:D.61, L:G.64, K:R.149 Salt bridges: L:K.19, L:D.122, K:R.149, K:R.149

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain B: S.20, T.38, D.61 Ligands: AF3.1, GDP.2 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.20, B:T.38, H2O.2, H2O.3 MG.6: 5 residues within 4Å: Chain D: S.20, T.38, D.61 Ligands: AF3.4, GDP.5 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:S.20, D:T.38, H2O.5, H2O.6 MG.9: 5 residues within 4Å: Chain F: S.20, T.38, D.61 Ligands: AF3.7, GDP.8 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:S.20, F:T.38, H2O.8, H2O.9 MG.12: 5 residues within 4Å: Chain H: S.20, T.38, D.61 Ligands: AF3.10, GDP.11 4 PLIP interactions: 2 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:S.20, H:T.38, H2O.11, H2O.12 MG.15: 5 residues within 4Å: Chain J: S.20, T.38, D.61 Ligands: AF3.13, GDP.14 4 PLIP interactions: 2 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:S.20, J:T.38, H2O.14, H2O.15 MG.18: 5 residues within 4Å: Chain L: S.20, T.38, D.61 Ligands: AF3.16, GDP.17 4 PLIP interactions: 2 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:S.20, L:T.38, H2O.17, H2O.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dong, N. et al., Structurally Distinct Bacterial TBC-like GAPs Link Arf GTPase to Rab1 Inactivation to Counteract Host Defenses. Cell(Cambridge,Mass.) (2012)

Release Date

2012-09-05

Peptides

Cysteine protease-like virA: ACEGIK
Ras-related protein Rab-1A: BDFHJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
A

I
C

K
E

B
B

D
D

F
F

H
B

J
D

L
F

Cysteine protease-like virA

Ras-related protein Rab-1A

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