SMTL ID : 4iru.1 (2 other biounits)

Crystal Structure of lepB GAP core in a transition state mimetic complex with Rab1A and ALF3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-oligomer

Ligands

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 3 residues within 4Å: Chain A: D.275, K.279, K.282 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.275 Salt bridges: A:K.282 ACT.2: 5 residues within 4Å: Chain A: I.41, L.43, L.44, K.161 Ligands: K.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.42, A:L.44 Salt bridges: A:K.161 ACT.16: 6 residues within 4Å: Chain A: E.174, N.175 Chain B: S.86, Y.87, R.89 Ligands: GOL.18 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:R.89 Hydrogen bonds: A:N.175 ACT.17: 4 residues within 4Å: Chain B: D.26, R.81, Q.111, W.112 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.112 Hydrogen bonds: B:Q.111 Salt bridges: B:R.81

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: L.5, T.6, L.7, L.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.6, A:L.8 GOL.4: 5 residues within 4Å: Chain A: R.71, T.75, P.76, Y.215, P.216 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.71, A:P.216 GOL.5: 4 residues within 4Å: Chain A: L.238, N.239, S.240, P.241 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.238, A:S.240 GOL.6: 5 residues within 4Å: Chain A: A.89, I.90, H.91 Chain B: D.99, T.101 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.89, A:H.91 GOL.7: 7 residues within 4Å: Chain A: H.93, S.119, R.120, R.272, T.273, D.274 Chain B: Y.47 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.273 Water bridges: A:N.239 GOL.8: 7 residues within 4Å: Chain A: S.211, E.212, S.240, P.241, K.242, P.243, S.244 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.242, A:K.242 GOL.18: 7 residues within 4Å: Chain B: K.20, Q.70, W.72, Y.87, R.89, G.90 Ligands: ACT.16 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.20, B:Q.70, B:Y.87, B:R.89, B:R.89

5 x K: POTASSIUM ION(Non-covalent)

K.9: 2 residues within 4Å: Chain A: E.212, N.239 No protein-ligand interaction detected (PLIP) K.10: 2 residues within 4Å: Chain A: N.39 Ligands: ACT.2 No protein-ligand interaction detected (PLIP) K.11: 4 residues within 4Å: Chain A: L.238, S.240, P.241, K.282 No protein-ligand interaction detected (PLIP) K.12: 1 residues within 4Å: Chain A: T.60 No protein-ligand interaction detected (PLIP) K.19: 3 residues within 4Å: Chain B: E.45, K.163 Ligands: GDP.14 No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.13: 4 residues within 4Å: Chain B: S.32, T.50 Ligands: GDP.14, AF3.15 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.32, B:T.50, H2O.1, H2O.1

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

GDP.14: 25 residues within 4Å: Chain A: H.91, R.120 Chain B: D.26, S.27, G.28, V.29, G.30, K.31, S.32, C.33, Y.43, E.45, S.46, Y.47, I.48, N.131, K.132, D.134, L.135, S.161, A.162, K.163 Ligands: MG.13, AF3.15, K.19 21 PLIP interactions: 18 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.26, B:G.28, B:V.29, B:G.30, B:K.31, B:S.32, B:S.32, B:C.33, B:Y.43, B:E.45, B:N.131, B:K.132, B:K.132, B:A.162, B:K.163 Water bridges: B:S.32, A:R.120 Salt bridges: B:K.31, B:D.134, A:R.120, A:R.120

1 x AF3: ALUMINUM FLUORIDE(Non-covalent)

AF3.15: 13 residues within 4Å: Chain A: R.120 Chain B: D.26, S.27, G.28, K.31, S.49, T.50, T.74, A.75, G.76, Q.77 Ligands: MG.13, GDP.14 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mishra, A.K. et al., The Legionella pneumophila GTPase Activating Protein LepB Accelerates Rab1 Deactivation by a Non-canonical Hydrolytic Mechanism. J.Biol.Chem. (2013)

Release Date

2013-07-10

Peptides

LepB: A
Ras-related protein Rab-1A: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

LepB

Ras-related protein Rab-1A

Related Entries With Identical Sequence