SMTL ID : 6vs4.1

Crystal structure of ADP RIBOSYLATION FACTOR-LIKE GTP BINDING PROTEIN /Small COPII coat GTPase SAR1 from Encephalitozoon cuniculi in complex with GDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 5 residues within 4Å: Chain A: G.14, K.17 Chain B: T.21, Y.24, G.196 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.17 PEG.4: 5 residues within 4Å: Chain A: T.21, Y.24, G.196 Chain B: G.14, K.17 No protein-ligand interaction detected (PLIP) PEG.5: 2 residues within 4Å: Chain B: H.93, T.94 No protein-ligand interaction detected (PLIP) PEG.8: 5 residues within 4Å: Chain C: G.14, K.17 Chain D: T.21, Y.24, G.196 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.17 PEG.11: 5 residues within 4Å: Chain C: T.21, Y.24, G.196 Chain D: G.14, K.17 No protein-ligand interaction detected (PLIP) PEG.12: 2 residues within 4Å: Chain D: H.93, T.94 No protein-ligand interaction detected (PLIP)

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

GDP.2: 16 residues within 4Å: Chain A: D.48, N.49, A.50, G.51, K.52, T.53, T.54, D.89, N.146, K.147, D.149, L.150, T.192, I.193, T.194 Ligands: MG.3 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:N.49, A:A.50, A:G.51, A:K.52, A:T.53, A:T.53, A:T.54, A:T.54, A:D.89, A:N.146, A:K.147, A:K.147, A:I.193, A:T.194, A:T.194 Water bridges: A:K.52, A:K.52 Salt bridges: A:K.52, A:D.149 GDP.6: 17 residues within 4Å: Chain B: I.47, D.48, N.49, A.50, G.51, K.52, T.53, T.54, D.89, N.146, K.147, D.149, L.150, T.192, I.193, T.194 Ligands: MG.7 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:N.49, B:A.50, B:G.51, B:K.52, B:T.53, B:T.54, B:T.54, B:D.89, B:N.146, B:K.147, B:K.147, B:I.193, B:T.194, B:T.194 Water bridges: B:K.52, B:T.53, B:T.53, B:D.89, B:D.89 Salt bridges: B:K.52, B:D.149 GDP.9: 16 residues within 4Å: Chain C: D.48, N.49, A.50, G.51, K.52, T.53, T.54, D.89, N.146, K.147, D.149, L.150, T.192, I.193, T.194 Ligands: MG.10 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:N.49, C:A.50, C:G.51, C:K.52, C:T.53, C:T.54, C:T.54, C:D.89, C:N.146, C:K.147, C:K.147, C:I.193, C:T.194 Water bridges: C:K.52, C:K.52 Salt bridges: C:K.52, C:D.149 GDP.13: 17 residues within 4Å: Chain D: I.47, D.48, N.49, A.50, G.51, K.52, T.53, T.54, D.89, N.146, K.147, D.149, L.150, T.192, I.193, T.194 Ligands: MG.14 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:N.49, D:A.50, D:G.51, D:K.52, D:T.53, D:T.53, D:T.54, D:T.54, D:D.89, D:N.146, D:K.147, D:K.147, D:I.193, D:T.194 Water bridges: D:K.52, D:D.89, D:D.89 Salt bridges: D:K.52, D:D.149

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: T.53, D.89 Ligands: GDP.2 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.53, H2O.1, H2O.1 MG.7: 3 residues within 4Å: Chain B: T.53, D.89 Ligands: GDP.6 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:T.53, H2O.2, H2O.3, H2O.3, H2O.3 MG.10: 3 residues within 4Å: Chain C: T.53, D.89 Ligands: GDP.9 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:T.53, H2O.4, H2O.4 MG.14: 3 residues within 4Å: Chain D: T.53, D.89 Ligands: GDP.13 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:T.53, H2O.5, H2O.6, H2O.6, H2O.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J. et al., Crystal structure of ADP RIBOSYLATION FACTOR-LIKE GTP BINDING PROTEIN /Small COPII coat GTPase SAR1 from Encephalitozoon cuniculi in complex with GDP. to be published

Release Date

2020-03-11

Peptides

Small COPII coat GTPase SAR1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Small COPII coat GTPase SAR1