SMTL ID : 7aw6.2 (1 other biounit)

The extracellular region of CD33 with bound sialoside analogue P22

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

5 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 2 residues within 4Å: Chain A: N.220, T.237 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.220, A:Q.239 NAG.2: 6 residues within 4Å: Chain A: N.124, G.125, S.126, S.146, V.147, H.148 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.126 Water bridges: A:N.124, A:N.124, A:S.126 NAG.3: 3 residues within 4Å: Chain A: I.160, Q.239, N.241 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.160 Hydrogen bonds: A:Q.239 Water bridges: A:Q.239, A:N.241, A:N.241, A:N.241 NAG.4: 5 residues within 4Å: Chain A: L.49, L.104, G.105, N.111, S.113 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.111 Water bridges: A:N.111, A:S.113, A:S.113 NAG.5: 2 residues within 4Å: Chain A: S.169, N.171 No protein-ligand interaction detected (PLIP)

1 x FVP: 2-aminoethyl 5-{[(4-cyclohexyl-1H-1,2,3-triazol-1-yl)acetyl]amino}-3,5,9-trideoxy-9-[(4-hydroxy-3,5-dimethylbenzene-1-carbonyl)amino]-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl-(2->6)-beta-D-galactopyranosyl-(1->4)-beta-D-glucopyranoside(Non-covalent)

FVP.6: 13 residues within 4Å: Chain A: F.32, P.57, P.59, Y.61, F.128, R.130, K.137, Y.138, S.139, Y.140, K.141, Q.144 Ligands: EDO.9 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:P.57, A:P.59, A:F.128, A:K.141, A:K.141 Hydrogen bonds: A:K.137, A:S.139, A:S.139, A:Q.144 Water bridges: A:S.135, A:K.137, A:K.137 Salt bridges: A:R.130

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.7: 5 residues within 4Å: Chain A: R.73, E.74, A.76, D.81, Q.94 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.81, A:Q.94 Water bridges: A:R.73, A:D.81 Salt bridges: A:R.73

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

EDO.8: 3 residues within 4Å: Chain A: T.202, T.203, H.204 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.204 Water bridges: A:T.203, A:T.203 EDO.9: 4 residues within 4Å: Chain A: I.78, F.128, S.139 Ligands: FVP.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.139, A:S.139

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bradshaw, W.J. et al., The extracellular region of CD33 with bound sialoside analogue P22. To Be Published

Release Date

2020-12-16

Peptides

Myeloid cell surface antigen CD33: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Myeloid cell surface antigen CD33

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