SMTL ID : 4z9s.1

Non-covalent assembly of monoubiquitin that mimics K11 poly-ubiquitin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

6 x MLA: MALONIC ACID(Non-covalent)

MLA.1: 6 residues within 4Å: Chain A: P.37, D.39, Q.40, R.74 Chain D: G.35 Ligands: SCN.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.40, A:R.74 Salt bridges: A:R.74 MLA.2: 8 residues within 4Å: Chain A: L.15, E.16, K.29, D.32, K.33 Chain B: E.24, D.52, G.53 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:D.52, B:G.53, A:E.16, A:E.16, A:D.32 Hydrophobic interactions: A:L.15 Salt bridges: A:K.29, A:K.33 MLA.7: 8 residues within 4Å: Chain A: K.33 Chain B: K.27, R.42, Q.49, L.50, E.51, D.52, R.72 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.49, B:D.52 Water bridges: B:K.27, B:K.27 Salt bridges: B:K.27, B:K.27, B:R.42, B:R.72, A:K.33 MLA.10: 9 residues within 4Å: Chain B: T.14, L.15, E.16, K.33 Chain C: E.51, D.52, G.53, R.54 Ligands: SCN.9 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:E.16, C:E.51 Salt bridges: B:K.33, B:K.33, C:R.54 Hydrophobic interactions: C:E.51 MLA.11: 5 residues within 4Å: Chain B: G.35 Chain C: P.37, D.39, Q.40, R.74 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:Q.40 Salt bridges: C:R.74 Water bridges: B:G.35 MLA.14: 8 residues within 4Å: Chain C: K.33 Chain D: K.27, R.42, Q.49, L.50, E.51, D.52, R.72 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:Q.49, D:D.52, D:D.52 Water bridges: D:K.27, D:L.50 Salt bridges: D:K.27, D:K.27, D:R.42, D:R.72, D:R.72, C:K.33

9 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.3: 6 residues within 4Å: Chain A: R.42, Q.49, E.51, D.52, R.72 Chain D: K.33 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:K.33, A:D.52 SCN.4: 4 residues within 4Å: Chain A: F.4, K.6, E.64, T.66 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.6 SCN.5: 2 residues within 4Å: Chain A: T.7, T.9 No protein-ligand interaction detected (PLIP) SCN.6: 3 residues within 4Å: Chain A: K.48, D.58, Y.59 No protein-ligand interaction detected (PLIP) SCN.8: 1 residues within 4Å: Chain B: L.71 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.71 SCN.9: 7 residues within 4Å: Chain B: K.33 Chain C: K.27, R.42, E.51, D.52, R.72 Ligands: MLA.10 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:K.33, C:D.52 SCN.12: 4 residues within 4Å: Chain C: L.15, E.16, K.33 Chain D: G.53 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:D.52, D:G.53, C:K.33 SCN.13: 1 residues within 4Å: Chain C: E.16 No protein-ligand interaction detected (PLIP) SCN.15: 3 residues within 4Å: Chain D: P.37, Q.40 Ligands: MLA.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Levin-Kravets, O. et al., Tetrameric Assembly of Monoubiquitin Accurately Mimics the Lys11 Polyubiquitin Chain Structure. Biochemistry (2015)

Release Date

2015-07-29

Peptides

Ubiquitin-40S ribosomal protein S27a: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Ubiquitin-40S ribosomal protein S27a

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