SMTL ID : 4txr.1

Crystal structure of LIP5 N-terminal domain complexed with CHMP1B MIM and CHMP5 MIM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.00 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

ACT.1: 9 residues within 4Å: Chain B: E.92, A.95, L.96, F.99, I.126, I.129, E.138, N.139, H.142 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.95, B:I.126 Salt bridges: B:H.142

9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 9 residues within 4Å: Chain B: C.88, E.92, I.129, F.132, G.133, E.134, L.135, T.136, N.139 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.92, B:F.132 EDO.3: 9 residues within 4Å: Chain B: P.7, L.8, L.22, R.23, A.25, Q.26, R.40, L.64, Q.67 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.22, B:Q.26, B:R.40, B:R.40, B:Q.67 EDO.4: 2 residues within 4Å: Chain B: E.56, K.59 4 PLIP interactions: 4 interactions with chain B Water bridges: B:P.55, B:E.56, B:E.56, B:E.56 EDO.5: 1 residues within 4Å: Chain B: K.158 No protein-ligand interaction detected (PLIP) EDO.6: 6 residues within 4Å: Chain B: M.48, K.49, I.50, D.51, S.52, K.53 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.52, B:S.52 EDO.7: 3 residues within 4Å: Chain B: E.69, A.70, K.73 2 PLIP interactions: 2 interactions with chain B Water bridges: B:A.70, B:K.73 EDO.8: 4 residues within 4Å: Chain B: Q.19, H.20 Chain C: D.35, L.38 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Q.19, C:D.35 EDO.9: 2 residues within 4Å: Chain B: N.159, E.161 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.159 EDO.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vild, C.J. et al., A Novel Mechanism of Regulating the ATPase VPS4 by Its Cofactor LIP5 and the Endosomal Sorting Complex Required for Transport (ESCRT)-III Protein CHMP5. J.Biol.Chem. (2015)

Release Date

2015-02-11

Peptides

Charged multivesicular body protein 1b: A
Vacuolar protein sorting-associated protein VTA1 homolog: B
Charged multivesicular body protein 5: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

Charged multivesicular body protein 1b

Vacuolar protein sorting-associated protein VTA1 homolog

Charged multivesicular body protein 5

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