SMTL ID : 5sby.1

CD44 PanDDA analysis group deposition -- The hyaluronan-binding domain of CD44 in complex with Z1878656559

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.22 Å

Oligo State

monomer

Ligands

1 x 8BI: (1R,2R)-2,4,4-trimethyl-N-[(1H-pyrazol-3-yl)methyl]cyclopentan-1-amine

8BI.1: 9 residues within 4Å: Chain A: R.11, F.16, F.38, N.103, D.111, T.113, S.114, V.115, P.119 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:R.11, A:F.16, A:N.103, A:V.115, A:P.119 Hydrogen bonds: A:R.11, A:S.114 Water bridges: A:S.114, A:T.116, A:T.116

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

PEG.2: 8 residues within 4Å: Chain A: Y.24, C.59, R.60, Y.61, I.70, I.78, C.79, A.80 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.24, A:R.60, A:Y.61, A:A.80 Water bridges: A:A.81

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

DMS.3: 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.4: 2 residues within 4Å: Chain A: H.83, T.84 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.84 Water bridges: A:T.84 DMS.5: 3 residues within 4Å: Chain A: T.44, M.45, E.65 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.45 Water bridges: A:D.46

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

EDO.6: 5 residues within 4Å: Chain A: N.39, T.41, F.102, N.103, A.104 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.41, A:A.104

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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