SMTL ID : 5ee5.1

Structure of human ARL1 in complex with the DCB domain of BIG1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

hetero-oligomer

Ligands

14 x NA: SODIUM ION(Non-functional Binders)

NA.1: 1 residues within 4Å: Chain A: T.82 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.82 NA.2: 4 residues within 4Å: Chain A: N.171, I.173, N.174 Chain B: Q.54 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.54, A:N.171, A:N.174 NA.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.4: 2 residues within 4Å: Chain A: E.50, Q.54 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.54 NA.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.6: 2 residues within 4Å: Chain A: E.41, L.44 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.41 NA.19: 1 residues within 4Å: Chain B: E.102 No protein-ligand interaction detected (PLIP) NA.20: 1 residues within 4Å: Chain B: D.140 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.140 NA.21: 2 residues within 4Å: Chain B: V.29, E.31 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.30 NA.22: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.23: 1 residues within 4Å: Chain B: E.104 No protein-ligand interaction detected (PLIP) NA.24: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.25: 2 residues within 4Å: Chain B: C.85, R.87 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.87 NA.26: 1 residues within 4Å: Chain B: E.161 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.161

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 3 residues within 4Å: Chain A: Y.166, L.167, Q.175 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.166 GOL.27: 4 residues within 4Å: Chain B: R.65, P.66, E.96, A.99 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.65

7 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 3 residues within 4Å: Chain A: T.183, L.186, N.187 Ligand excluded by PLIP CL.9: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain A: D.128 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain A: N.164 Ligand excluded by PLIP CL.12: 6 residues within 4Å: Chain A: L.84, D.85, Q.88, Q.134, K.137, A.138 Ligand excluded by PLIP CL.13: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.28: 3 residues within 4Å: Chain B: A.109, R.141, K.142 Ligand excluded by PLIP

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.14: 21 residues within 4Å: Chain B: D.16, G.17, A.18, G.19, K.20, T.21, T.22, T.35, P.37, T.38, G.59, G.60, N.116, K.117, D.119, M.120, S.149, A.150, T.151 Ligands: MG.15, MG.18 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:G.17, B:A.18, B:G.19, B:K.20, B:T.21, B:T.22, B:T.22, B:T.35, B:T.38, B:G.60, B:N.116, B:K.117, B:K.117, B:A.150, B:T.151 Water bridges: B:T.22, B:T.35 Salt bridges: B:K.20, B:K.20, B:D.119

4 x MG: MAGNESIUM ION(Non-covalent)

MG.15: 6 residues within 4Å: Chain B: T.21, T.38, D.57, L.58 Ligands: GTP.14, MG.18 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.21, B:T.38 MG.16: 4 residues within 4Å: Chain B: D.16, D.83, D.86, R.89 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.83, B:D.86 MG.17: 6 residues within 4Å: Chain B: V.46, T.47, Y.48, N.50, L.51, K.52 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:L.51 MG.18: 5 residues within 4Å: Chain B: T.21, I.36, T.38 Ligands: GTP.14, MG.15 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.21, B:T.38

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

ACT.29: 1 residues within 4Å: Chain B: Y.67 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Galindo, A. et al., Structural Insights into Arl1-Mediated Targeting of the Arf-GEF BIG1 to the trans-Golgi. Cell Rep (2016)

Release Date

2016-07-06

Peptides

Brefeldin A-inhibited guanine nucleotide-exchange protein 1: A
ADP-ribosylation factor-like protein 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Brefeldin A-inhibited guanine nucleotide-exchange protein 1

ADP-ribosylation factor-like protein 1

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