SMTL ID : 5fw5.1

Crystal structure of human G3BP1 in complex with Semliki Forest Virus nsP3-25 comprising two FGDF motives

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

hetero-4-2-mer

Ligands

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: R.79, L.98, R.108 Ligands: GOL.10 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Water bridges: A:R.79, A:R.79, B:Q.135 Salt bridges: A:R.79, A:R.108 SO4.2: 2 residues within 4Å: Chain A: K.77, R.79 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.77, A:R.79 Salt bridges: A:K.77, A:R.79 SO4.4: 2 residues within 4Å: Chain B: R.79, L.98 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:F.139, B:R.79 Salt bridges: B:R.79 SO4.5: 6 residues within 4Å: Chain B: G.36, K.37, G.58, Q.59, K.60, E.61 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.59, B:K.60 Salt bridges: B:K.60 SO4.13: 4 residues within 4Å: Chain D: R.79, L.98, R.108 Ligands: GOL.22 5 PLIP interactions: 1 interactions with chain E, 4 interactions with chain D Water bridges: E:Q.135, D:R.79, D:R.79 Salt bridges: D:R.79, D:R.108 SO4.14: 2 residues within 4Å: Chain D: K.77, R.79 4 PLIP interactions: 4 interactions with chain D Water bridges: D:K.77, D:R.79 Salt bridges: D:K.77, D:R.79 SO4.16: 2 residues within 4Å: Chain E: R.79, L.98 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain E Water bridges: D:F.139, E:R.79 Salt bridges: E:R.79 SO4.17: 6 residues within 4Å: Chain E: G.36, K.37, G.58, Q.59, K.60, E.61 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Q.59, E:K.60 Salt bridges: E:K.60

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

ACT.3: 2 residues within 4Å: Chain A: K.6, P.9 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.6 ACT.6: 5 residues within 4Å: Chain B: Q.19, L.23, F.34 Chain F: F.23 Ligands: GOL.7 No protein-ligand interaction detected (PLIP) ACT.15: 2 residues within 4Å: Chain D: K.6, P.9 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:K.6 ACT.18: 4 residues within 4Å: Chain E: Q.19, L.23, F.34 Ligands: GOL.19 No protein-ligand interaction detected (PLIP)

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain B: Q.19, T.22, L.23, F.34 Ligands: ACT.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.23 Water bridges: B:E.15, B:Q.19 GOL.8: 6 residues within 4Å: Chain B: Y.21, T.22, N.25, C.74, H.75, T.76 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.22, B:T.76, B:T.76 Water bridges: B:N.25 GOL.9: 10 residues within 4Å: Chain B: P.7, S.8, P.9, V.12, A.85, T.86, D.89, G.90, V.91, F.125 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.7, B:T.86, B:D.89 Water bridges: B:D.89 GOL.10: 2 residues within 4Å: Chain B: D.136 Ligands: SO4.1 No protein-ligand interaction detected (PLIP) GOL.19: 5 residues within 4Å: Chain E: Q.19, T.22, L.23, F.34 Ligands: ACT.18 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:L.23 Water bridges: E:Q.19 GOL.20: 6 residues within 4Å: Chain E: Y.21, T.22, N.25, C.74, H.75, T.76 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:T.22, E:T.76, E:T.76 Water bridges: E:N.25 GOL.21: 10 residues within 4Å: Chain E: P.7, S.8, P.9, V.12, A.85, T.86, D.89, G.90, V.91, F.125 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:P.7, E:T.86, E:D.89, E:D.89 Water bridges: E:D.89 GOL.22: 2 residues within 4Å: Chain E: D.136 Ligands: SO4.13 No protein-ligand interaction detected (PLIP)

4 x K: POTASSIUM ION(Non-covalent)

K.11: 3 residues within 4Å: Chain B: A.27, P.28, D.29 No protein-ligand interaction detected (PLIP) K.12: 4 residues within 4Å: Chain A: Y.57 Chain B: P.9, H.84, A.85 No protein-ligand interaction detected (PLIP) K.23: 3 residues within 4Å: Chain E: A.27, P.28, D.29 No protein-ligand interaction detected (PLIP) K.24: 4 residues within 4Å: Chain D: Y.57 Chain E: P.9, H.84, A.85 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schulte, T. et al., Combined structural, biochemical and cellular evidence demonstrates that both FGDF motifs in alphavirus nsP3 are required for efficient replication. Open Biol (2016)

Release Date

2016-07-20

Peptides

RAS GTPASE-ACTIVATING PROTEIN-BINDING PROTEIN 1: ABDE
NON-STRUCTURAL PROTEIN 3: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
A

E
B

C
C

F
C

RAS GTPASE-ACTIVATING PROTEIN-BINDING PROTEIN 1

NON-STRUCTURAL PROTEIN 3

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