SMTL ID : 5sc7.1

CD44 PanDDA analysis group deposition -- The hyaluronan-binding domain of CD44 in complex with POB0120

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

monomer

Ligands

1 x W2M: (2R)-1',4'-dihydro-2'H-spiro[pyrrolidine-2,3'-quinolin]-2'-one(Non-covalent)

W2M.1: 6 residues within 4Å: Chain A: N.7, V.8, V.131, N.132, R.133 Ligands: SO4.9 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:N.7, A:R.133 Water bridges: A:N.7, A:E.19, A:R.133

5 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 7 residues within 4Å: Chain A: C.10, C.112, T.113, S.114, N.132, R.133, D.134 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.133, A:D.134 Salt bridges: A:D.134 DMS.3: 2 residues within 4Å: Chain A: H.83, T.84 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.84 DMS.4: 2 residues within 4Å: Chain A: S.139, K.140 No protein-ligand interaction detected (PLIP) DMS.5: 7 residues within 4Å: Chain A: R.11, F.16, F.38, S.40, N.103, A.106 Ligands: DMS.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.40, A:N.103 DMS.6: 6 residues within 4Å: Chain A: V.8, R.11, F.16, F.38, V.115 Ligands: DMS.5 No protein-ligand interaction detected (PLIP)

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

EDO.7: 5 residues within 4Å: Chain A: N.39, T.41, F.102, N.103, A.104 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.41, A:A.104 Water bridges: A:N.103, A:S.105, A:S.105 EDO.8: 3 residues within 4Å: Chain A: N.39, N.103, P.119 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.103 Water bridges: A:F.38, A:N.39, A:N.39

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

SO4.9: 3 residues within 4Å: Chain A: N.7, G.22 Ligands: W2M.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.7 Water bridges: A:E.19, A:E.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bradshaw, W.J. et al., CD44 PanDDA analysis group deposition. To Be Published

Release Date

2021-09-22

Peptides

CD44 antigen: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

CD44 antigen

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