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

Crystal structure of Mn2+ bound calprotectin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-2-2-mer

Ligands

6 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.59, N.61, D.63, A.65, E.70 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.59, A:D.63, A:A.65, A:E.70, H2O.1 CA.4: 5 residues within 4Å: Chain B: D.67, N.69, D.71, Q.73, E.78 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.67, B:D.71, B:Q.73, B:E.78, H2O.3 CA.5: 5 residues within 4Å: Chain B: S.23, L.26, H.28, T.31, E.36 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.23, B:L.26, B:H.28, B:T.31, H2O.4 CA.8: 5 residues within 4Å: Chain C: D.59, N.61, D.63, A.65, E.70 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.59, C:D.63, C:A.65, C:E.70, H2O.7 CA.13: 5 residues within 4Å: Chain D: D.67, N.69, D.71, Q.73, E.78 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.67, D:D.71, D:Q.73, D:E.78, H2O.10 CA.14: 5 residues within 4Å: Chain D: S.23, L.26, H.28, T.31, E.36 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:S.23, D:L.26, D:H.28, D:T.31, H2O.9

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 6 residues within 4Å: Chain A: H.17, H.27 Chain B: H.91, H.95, H.103, H.105 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Metal complexes: A:H.17, A:H.27, B:H.91, B:H.95, B:H.103, B:H.105 MN.3: 4 residues within 4Å: Chain A: H.83, H.87 Chain B: H.20, D.30 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Metal complexes: B:H.20, B:D.30, A:H.83, A:H.87 MN.10: 4 residues within 4Å: Chain C: H.83, H.87 Chain D: H.20, D.30 5 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: D:D.30, D:D.30, C:H.83, C:H.87, H2O.10 MN.11: 6 residues within 4Å: Chain C: H.17, H.27 Chain D: H.91, H.95, H.103, H.105 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Metal complexes: D:H.91, D:H.95, D:H.103, D:H.105, C:H.17, C:H.27

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 8 residues within 4Å: Chain A: H.27, F.68 Chain B: W.88, H.91, E.92, H.95 Chain D: D.65, R.85 8 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: D:R.85, B:H.91, B:E.92 Water bridges: D:H.61, D:R.85, A:Q.69, A:Q.69, B:H.95 GOL.9: 8 residues within 4Å: Chain A: E.57, I.60, I.73, K.77 Chain C: E.57, I.60, I.73, K.77 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.77, A:K.77

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

SO4.7: 4 residues within 4Å: Chain C: K.35, G.50, A.51, D.52 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:A.51, C:D.52, C:D.52 Water bridges: C:V.53 Salt bridges: C:K.35 SO4.12: 5 residues within 4Å: Chain D: L.26, G.27, H.28, N.33, Q.73 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:L.26, D:H.28, D:N.33, D:Q.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Damo, S.M. et al., Molecular basis for manganese sequestration by calprotectin and roles in the innate immune response to invading bacterial pathogens. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-02-20

Peptides

Protein S100-A8: AC
Protein S100-A9: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
K

B
C

D
L

Protein S100-A8

Protein S100-A9

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