SMTL ID : 8sjc.1

Crystal structure of Zn2+ bound calprotectin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

hetero-2-2-mer

Ligands

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.1: 19 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: M.77, A.80, R.81, W.84 Chain D: M.77, A.80, R.81, W.84 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.69, A:Q.69

9 x CA: CALCIUM ION(Non-covalent)

CA.2: 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.3: 5 residues within 4Å: Chain A: S.20, K.23, N.25, 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.5: 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.7: 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.8: 2 residues within 4Å: Chain C: Q.17, Y.18 No protein-ligand interaction detected (PLIP) CA.9: 1 residues within 4Å: Chain C: K.39 No protein-ligand interaction detected (PLIP) CA.10: 1 residues within 4Å: Chain C: E.88 No protein-ligand interaction detected (PLIP) CA.12: 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.10 CA.13: 8 residues within 4Å: Chain D: S.19, L.22, H.24, P.25, T.27, L.28, E.32, Q.69 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.10

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 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.3 MG.6: 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.6

2 x ZN: ZINC ION(Non-covalent)

ZN.11: 6 residues within 4Å: Chain A: H.17, H.27 Chain C: H.87, H.91, H.99, H.101 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain C Metal complexes: A:H.17, A:H.27, C:H.87, C:H.91, C:H.99, C:H.101 ZN.14: 6 residues within 4Å: Chain B: H.17, H.27 Chain D: H.87, H.91, H.99, H.101 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain B Metal complexes: D:H.87, D:H.91, D:H.99, D:H.101, B:H.17, B:H.27

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