SMTL ID : 5d65.1

X-RAY STRUCTURE OF MACROPHAGE INFLAMMATORY PROTEIN-1 ALPHA (CCL3) WITH HEPARIN COMPLEX

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-pentamer

Ligands

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

IDS-SGN.1: 8 residues within 4Å: Chain B: Q.22, N.23, I.25, A.26, K.45, L.66 Chain E: R.46 Ligands: IDS-SGN.2 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:Q.22, B:A.26, B:K.45 Salt bridges: E:R.46 IDS-SGN.2: 6 residues within 4Å: Chain B: Q.19, Q.22, N.23, K.61, D.65 Ligands: IDS-SGN.1 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.19, B:Q.22, B:Q.22, B:N.23, B:N.23, B:K.61 Salt bridges: B:K.61, B:K.61, B:K.61

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

BGC.3: 6 residues within 4Å: Chain A: I.25, A.26, D.65, L.66, S.69 Chain B: R.46 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.65, A:S.69, A:S.69, B:R.46, B:R.46 Salt bridges: A:K.45 BGC.4: 4 residues within 4Å: Chain A: S.36, P.38, D.53 Ligands: BGC.5 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.37 BGC.5: 4 residues within 4Å: Chain A: D.53, S.55, E.56 Ligands: BGC.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.55, A:S.55, A:S.55 BGC.6: 3 residues within 4Å: Chain A: Q.19, W.58, K.61 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.19, A:Q.19 BGC.7: 2 residues within 4Å: Chain A: Q.60 Chain B: P.21 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.60 BGC.9: 7 residues within 4Å: Chain C: Q.22, N.23, I.25, K.45, D.65, L.66, S.69 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.22, C:K.45, C:K.45, C:S.69 BGC.10: 12 residues within 4Å: Chain B: T.7, T.9, S.32, Q.34 Chain C: S.14 Chain D: A.4, A.5, D.6, T.7, T.9, Q.34 Chain E: S.14 9 PLIP interactions: 5 interactions with chain D, 1 interactions with chain E, 3 interactions with chain B Hydrogen bonds: D:D.6, D:T.7, D:T.9, D:T.9, D:Q.34, E:S.14, B:T.7, B:S.32, B:S.32 BGC.11: 3 residues within 4Å: Chain D: R.18, Q.19, F.24 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.18, D:R.18 Salt bridges: D:R.18 BGC.13: 1 residues within 4Å: Chain E: Q.19 No protein-ligand interaction detected (PLIP)

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

CL.8: 5 residues within 4Å: Chain B: C.35, S.36 Chain C: F.13, C.35, S.36 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain D: C.35, S.36 Chain E: F.13, S.36 Ligand excluded by PLIP

1 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.12: 6 residues within 4Å: Chain B: S.33, C.35, S.36, P.38 Chain E: S.17, R.18 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:C.35, B:S.36, E:S.17

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

2016-04-20

Peptides

C-C motif chemokine 3: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

C-C motif chemokine 3

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