SMTL ID : 4oik.1 (1 other biounit)

(Quasi-)Racemic X-ray crystal structure of glycosylated chemokine Ser-CCL1.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

NAG.1: 1 residues within 4Å: Chain A: N.30 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.30, A:E.38 NAG.10: 1 residues within 4Å: Chain B: N.30 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.30, B:E.38 Water bridges: B:N.30

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

SO4.2: 3 residues within 4Å: Chain A: T.31, S.32, S.33 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.33, A:S.33 Water bridges: A:I.34 SO4.3: 4 residues within 4Å: Chain A: V.56, G.57, W.58, R.61 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.19, A:W.58 Water bridges: A:R.61, A:R.61 Salt bridges: A:R.61 SO4.4: 5 residues within 4Å: Chain A: F.8, R.10 Chain B: F.8, R.10 Ligands: SO4.12 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.10, B:R.10 SO4.5: 4 residues within 4Å: Chain A: Y.28, L.66, R.67, H.68 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.68 Water bridges: A:Y.28, A:L.66, A:H.68 Salt bridges: A:R.67 SO4.6: 3 residues within 4Å: Chain A: E.19, R.61, H.62 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.19 Water bridges: A:H.62, A:H.62 Salt bridges: A:R.61, A:H.62 SO4.7: 2 residues within 4Å: Chain A: P.7 Chain B: S.14 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.14, A:P.7 Water bridges: B:S.14, B:S.14, B:S.14, A:S.9 SO4.8: 3 residues within 4Å: Chain A: P.21, L.22, R.23 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.22, A:R.23 SO4.9: 2 residues within 4Å: Chain A: S.14 Chain B: P.7 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:P.7 Water bridges: B:S.9, A:F.13, A:S.14, A:S.14 SO4.11: 0 residues within 4Å: (No contacts) 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:K.72, A:K.72 SO4.12: 5 residues within 4Å: Chain B: R.10, P.70, S.71, K.72 Ligands: SO4.4 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.10, B:S.71, B:K.72 Water bridges: B:R.10, B:R.29 SO4.13: 2 residues within 4Å: Chain B: S.32, S.33 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.32, B:S.33, B:S.33 Water bridges: B:I.34 SO4.14: 4 residues within 4Å: Chain B: V.56, G.57, W.58, R.61 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.58 Salt bridges: B:R.61 SO4.15: 4 residues within 4Å: Chain B: Y.28, L.66, R.67, H.68 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.68 Salt bridges: B:R.67 SO4.16: 3 residues within 4Å: Chain B: E.19, R.61, H.62 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.19 Water bridges: B:H.62, B:H.62 Salt bridges: B:R.61, B:H.62 SO4.17: 2 residues within 4Å: Chain B: L.22, R.23 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.23

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Okamoto, R. et al., (Quasi-)Racemic X-ray Structures of Glycosylated and Non-Glycosylated Forms of the Chemokine Ser-CCL1 Prepared by Total Chemical Synthesis. Angew.Chem.Int.Ed.Engl. (2014)

Release Date

2014-05-07

Peptides

C-C motif chemokine 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C-C motif chemokine 1

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