SMTL ID : 7lul.1

Structure of the MM2 Erbin PDZ variant in complex with a high-affinity peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

1 x ARG- TRP- TYR- GLU- ARG- TRP- VAL: peptide(Non-covalent)

ARG-TRP-TYR-GLU-ARG-TRP-VAL.1: 18 residues within 4Å: Chain A: E.14, L.15, G.16, F.17, S.18, I.19, S.20, R.26, G.27, N.28, P.29, T.40, R.41, Q.43, L.71, E.75, K.79 Ligands: PEG.6 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:F.17, A:R.26, A:P.29, A:T.40, A:R.41, A:Q.43, A:L.71 Hydrogen bonds: A:L.15, A:G.16, A:F.17, A:F.17, A:F.17, A:S.18, A:I.19, A:I.19, A:R.26, A:R.41, A:E.72 Water bridges: A:E.14, A:G.21, A:R.26, A:R.41, A:E.72, A:K.79 Salt bridges: A:R.41

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.2: 4 residues within 4Å: Chain A: N.62, G.63, Y.64, S.65 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.65

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

EDO.3: 2 residues within 4Å: Chain A: E.4, I.88 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.4 EDO.4: 4 residues within 4Å: Chain A: V.23, G.24, R.70, E.72 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.70

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

NA.5: 1 residues within 4Å: Chain A: D.12 No protein-ligand interaction detected (PLIP)

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

PEG.6: 5 residues within 4Å: Chain A: R.41 Ligands: ARG-TRP-TYR-GLU-ARG-TRP-VAL.1, ARG-TRP-TYR-GLU-ARG-TRP-VAL.1, ARG-TRP-TYR-GLU-ARG-TRP-VAL.1, ARG-TRP-TYR-GLU-ARG-TRP-VAL.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Teyra, J. et al., Comprehensive Assessment of the Relationship Between Site -2 Specificity and Helix alpha 2 in the Erbin PDZ Domain. J.Mol.Biol. (2021)

Release Date

2021-07-28

Peptides

Erbin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Erbin