SMTL ID : 8b87.1

Crystal structure of Scribble PDZ1 with human papillomavirus strain 16 E6 peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-2-2-mer

Ligands

1 x SDY: beta-D-talopyranose(Non-covalent)

SDY.1: 15 residues within 4Å: Chain A: K.57, G.58, D.59, D.60, F.64, K.84, W.117 Chain B: K.57, G.58, D.59, D.60, F.64, K.84, W.117 Ligands: PEG.9 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.60, B:D.59, B:D.59, B:D.60 Water bridges: A:K.57, A:K.57, A:D.59, A:D.59, A:K.84 Salt bridges: A:K.57

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

PEG.2: 11 residues within 4Å: Chain A: K.51, D.59, D.60, E.61, G.62, K.84, Q.94, G.95 Chain B: R.26, K.84 Ligands: PEG.9 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.60, A:D.60, A:E.61, A:K.84 Water bridges: A:G.95, B:K.84 PEG.3: 4 residues within 4Å: Chain A: N.89, G.90, A.111, Q.113 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.111 PEG.4: 5 residues within 4Å: Chain A: T.54, P.55, Y.56 Chain C: R.5 Ligands: PEG.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.55 PEG.5: 7 residues within 4Å: Chain A: T.54, P.55, Y.56, K.57, G.58 Chain B: I.27 Ligands: PEG.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.55, A:G.58 PEG.6: 2 residues within 4Å: Chain A: T.35, A.77 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.35 Water bridges: A:T.35 PEG.7: 3 residues within 4Å: Chain B: V.102, R.106 Chain D: T.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.106, B:R.106 PEG.8: 7 residues within 4Å: Chain A: E.119 Chain B: T.54, P.55, Y.56, K.57, G.58 Chain D: R.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.55, B:G.58 PEG.9: 12 residues within 4Å: Chain A: R.26, D.60, K.84 Chain B: K.51, D.59, D.60, E.61, G.62, K.84, G.95 Ligands: SDY.1, PEG.2 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:R.26, A:K.84, B:D.59, B:D.60, B:E.61, B:E.61, B:K.84 PEG.10: 3 residues within 4Å: Chain C: T.4, R.6 Ligands: NH4.11 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.6, C:R.6

1 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.11: 4 residues within 4Å: Chain A: H.98, H.99 Chain C: R.6 Ligands: PEG.10 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.6 Water bridges: A:H.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stewart, B.Z. et al., Crystal structure of Scribble PDZ1 with human papillomavirus strain 16 E6 peptide. To Be Published

Release Date

2023-10-18

Peptides

Protein scribble homolog: AB
Protein E6: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Protein scribble homolog

Protein E6

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