SMTL ID : 8sjb.1

Crystal structure of Zn2+ bound calprotectin variant H87C

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

hetero-2-2-mer

Ligands

8 x CA: CALCIUM ION(Non-covalent)

CA.1: 7 residues within 4Å: Chain A: D.59, N.61, D.63, A.65, V.66, N.67, 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.2: 6 residues within 4Å: Chain A: S.20, K.23, N.25, F.26, A.28, Y.30 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.20, A:K.23, A:N.25, A:A.28, H2O.1 CA.4: 7 residues within 4Å: Chain B: D.59, N.61, D.63, A.65, V.66, N.67, E.70 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.59, B:D.63, B:A.65, B:E.70, H2O.3 CA.5: 6 residues within 4Å: Chain B: S.20, K.23, N.25, F.26, A.28, Y.30 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.20, B:K.23, B:N.25, B:A.28, H2O.4 CA.8: 7 residues within 4Å: Chain C: D.63, N.65, D.67, Q.69, L.70, S.71, E.74 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.63, C:D.67, C:Q.69, C:E.74, H2O.6 CA.9: 8 residues within 4Å: Chain C: S.19, L.22, H.24, P.25, T.27, L.28, N.29, E.32 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:S.19, C:L.22, C:H.24, C:T.27, H2O.7 CA.10: 7 residues within 4Å: Chain D: D.63, N.65, D.67, Q.69, L.70, S.71, E.74 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.63, D:D.67, D:Q.69, D:E.74, H2O.9 CA.11: 7 residues within 4Å: Chain D: S.19, L.22, H.24, P.25, T.27, L.28, E.32 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:S.19, D:L.22, D:H.24, D:T.27, H2O.9

2 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)

2PE.3: 23 residues within 4Å: Chain A: I.60, Q.69, E.70, L.72, I.73, I.76 Chain B: I.60, Q.69, L.72, I.73, I.76 Chain C: A.80, R.81, L.82, W.84, A.85 Chain D: M.77, L.78, A.80, R.81, L.82, W.84, A.85 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Q.69, C:R.81 2PE.6: 12 residues within 4Å: Chain B: K.23, Y.30, R.31, D.32, K.35, A.51, D.52, D.63, G.64 Chain C: N.65, D.67, Q.69 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:N.65, B:R.31, B:D.52 Water bridges: B:K.35

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 4 residues within 4Å: Chain A: H.83, C.87 Chain C: H.16, D.26 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Metal complexes: C:H.16, C:D.26, C:D.26, A:H.83, A:C.87

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Perera, Y.R. et al., Crystal structure of Zn2+ bound calprotectin. To Be Published

Release Date

2024-07-03

Peptides

Protein S100-A8: AB
Protein S100-A9: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Protein S100-A8

Protein S100-A9