SMTL ID : 5dnf.1

Crystal structure of CC chemokine 5 (CCL5) oligomer in complex with heparin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-9-mer

Ligands

3 x SGN- IDS- SGN: 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose

SGN-IDS-SGN.1: 5 residues within 4Å: Chain C: E.51, K.52, K.53, W.54, R.56 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.53, C:R.56 Salt bridges: C:K.53, C:R.56, C:R.56 SGN-IDS-SGN.2: 5 residues within 4Å: Chain D: E.51, K.52, K.53, W.54, R.56 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.53, D:R.56 Salt bridges: D:K.53, D:R.56, D:R.56 SGN-IDS-SGN.3: 6 residues within 4Å: Chain I: E.51, K.52, K.53, W.54, R.56, E.57 4 PLIP interactions: 4 interactions with chain I Hydrogen bonds: I:K.53, I:K.53, I:R.56, I:E.57, I:E.57 Salt bridges: I:K.53, I:R.56, I:R.56

6 x GLA: alpha-D-galactopyranose(Post Translational Modification)

GLA.4: 7 residues within 4Å: Chain A: S.1, S.2 Chain D: P.6, E.23, F.25, Q.45 Ligands: BGC.5 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:E.23, D:Q.45 Water bridges: A:S.2, A:S.2 GLA.12: 7 residues within 4Å: Chain C: S.1, S.2 Chain F: P.6, E.23, F.25, Q.45 Ligands: BGC.13 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain C Hydrogen bonds: F:E.23, C:S.2 GLA.18: 6 residues within 4Å: Chain A: P.6, E.23, F.25, Q.45 Chain D: S.1, S.2 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:E.23, D:S.2 Water bridges: A:T.4, D:S.2 GLA.24: 5 residues within 4Å: Chain C: P.6, F.25, Q.45 Chain F: S.1, S.2 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain C Water bridges: F:S.2, C:Q.45 Hydrogen bonds: C:Q.45 GLA.33: 6 residues within 4Å: Chain H: S.1, S.2 Chain I: P.6, E.23, F.25, Q.45 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain I Hydrogen bonds: H:S.2, H:S.2, I:E.23, I:Q.45 GLA.38: 7 residues within 4Å: Chain H: P.6, E.23, F.25, Q.45 Chain I: S.1, S.2 Ligands: BGC.34 3 PLIP interactions: 1 interactions with chain I, 2 interactions with chain H Hydrogen bonds: I:S.2, H:E.23 Water bridges: H:T.4

5 x BGC: beta-D-glucopyranose(Non-covalent)

BGC.5: 9 residues within 4Å: Chain A: S.2, D.3, T.5, S.28 Chain D: S.2, D.3, T.5, S.28 Ligands: GLA.4 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:D.3, D:D.3, D:S.28, D:S.28, A:T.5, A:S.28 Water bridges: A:S.2 BGC.13: 8 residues within 4Å: Chain C: D.3, T.5, S.28, K.30 Chain F: D.3, T.5, S.28 Ligands: GLA.12 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:T.5, C:S.28, C:S.28, F:S.28 BGC.21: 5 residues within 4Å: Chain E: Y.24, E.63 Chain G: Y.24, Y.26, E.63 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Y.24, E:E.63 Water bridges: E:Y.26 BGC.29: 4 residues within 4Å: Chain G: P.6, E.23, F.25, Q.45 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:Q.45 BGC.34: 10 residues within 4Å: Chain H: S.2, D.3, T.5, S.28, K.30 Chain I: S.2, T.5, S.28, K.30 Ligands: GLA.38 6 PLIP interactions: 4 interactions with chain H, 2 interactions with chain I Hydrogen bonds: H:S.2, H:T.5, H:S.28, H:S.28, I:S.28, I:S.28

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

SO4.6: 5 residues within 4Å: Chain A: E.51, K.52, K.53, R.56 Ligands: CL.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.53, A:R.56 Salt bridges: A:K.52 SO4.22: 2 residues within 4Å: Chain E: K.52, K.53 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.53 Salt bridges: E:K.52 SO4.25: 4 residues within 4Å: Chain F: K.52, K.53, W.54 Ligands: CL.28 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:K.53, F:W.54 Salt bridges: F:K.52 SO4.30: 2 residues within 4Å: Chain G: K.52, K.53 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:K.53 Salt bridges: G:K.52 SO4.35: 4 residues within 4Å: Chain H: E.51, K.52, K.53 Ligands: CL.36 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:K.53 Salt bridges: H:K.52

20 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 4 residues within 4Å: Chain A: F.9, C.31, S.32 Chain B: S.32 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: W.54 Ligands: SO4.6 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain B: R.18, I.21 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain B: K.53 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain C: F.9, S.32 Chain D: F.9, S.32 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain C: R.18, I.21 Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain C: K.52 Ligand excluded by PLIP CL.17: 5 residues within 4Å: Chain C: R.56, I.59, N.60 Chain E: P.17, H.20 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain D: R.18, I.21 Ligand excluded by PLIP CL.20: 1 residues within 4Å: Chain D: K.52 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain E: R.18, I.21 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain E: S.32 Chain F: F.9, S.32 Ligand excluded by PLIP CL.27: 2 residues within 4Å: Chain F: Y.11, N.49 Ligand excluded by PLIP CL.28: 3 residues within 4Å: Chain F: K.52, K.53 Ligands: SO4.25 Ligand excluded by PLIP CL.31: 2 residues within 4Å: Chain G: R.18, I.21 Ligand excluded by PLIP CL.32: 1 residues within 4Å: Chain G: M.64 Ligand excluded by PLIP CL.36: 3 residues within 4Å: Chain H: K.53, W.54 Ligands: SO4.35 Ligand excluded by PLIP CL.37: 3 residues within 4Å: Chain G: S.32 Chain H: F.9, S.32 Ligand excluded by PLIP CL.39: 2 residues within 4Å: Chain I: R.18, I.21 Ligand excluded by PLIP CL.40: 2 residues within 4Å: Chain I: N.49, K.52 Ligand excluded by PLIP

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.11: 3 residues within 4Å: Chain B: Y.24, F.25, E.63 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.24

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liang, W.G. et al., Structural basis for oligomerization and glycosaminoglycan binding of CCL5 and CCL3. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-04-13

Peptides

C-C motif chemokine 5: ABCDEFGHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

C-C motif chemokine 5

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