SMTL ID : 7quv.1

Crystal structure of human Calprotectin (S100A8/S100A9) in complex with Peptide 3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

hetero-2-2-2-mer

Ligands

6 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.69, N.71, D.73, Q.75, E.80 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.69, A:D.73, A:Q.75, A:E.80, H2O.2 CA.2: 5 residues within 4Å: Chain A: S.25, L.28, H.30, T.33, E.38 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:S.25, A:L.28, A:H.30, A:T.33, A:E.38 CA.6: 5 residues within 4Å: Chain B: D.61, N.63, D.65, A.67, E.72 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.61, B:D.65, B:A.67, B:E.72, H2O.2 CA.12: 5 residues within 4Å: Chain D: D.69, N.71, D.73, Q.75, E.80 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.69, D:D.73, D:Q.75, D:E.80, H2O.5 CA.13: 5 residues within 4Å: Chain D: S.25, L.28, H.30, T.33, E.38 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:S.25, D:L.28, D:H.30, D:T.33, D:E.38 CA.17: 5 residues within 4Å: Chain E: D.61, N.63, D.65, A.67, E.72 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.61, E:D.65, E:A.67, E:E.72, H2O.6

2 x NI: NICKEL (II) ION(Non-covalent)

NI.3: 6 residues within 4Å: Chain A: H.93, H.97, H.105, H.107 Chain B: H.19, H.29 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Metal complexes: A:H.93, A:H.97, A:H.105, A:H.107, B:H.19, B:H.29 NI.14: 6 residues within 4Å: Chain D: H.93, H.97, H.105, H.107 Chain E: H.19, H.29 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain E Metal complexes: D:H.93, D:H.97, D:H.105, D:H.107, E:H.19, E:H.29

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 8 residues within 4Å: Chain A: A.86, R.87, W.90 Chain D: R.87, W.90 Ligands: EDO.9, PGE.15, EDO.20 No protein-ligand interaction detected (PLIP) PGE.15: 8 residues within 4Å: Chain A: R.87, W.90 Chain D: A.86, R.87, W.90 Ligands: PGE.4, EDO.9, EDO.20 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: H.93, E.94, H.97 Chain B: H.29 Chain D: D.67, R.87 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:H.93, D:R.87 Water bridges: A:E.94, A:E.94, A:H.97, D:R.87 GOL.16: 6 residues within 4Å: Chain A: D.67, R.87 Chain D: H.93, E.94, H.97 Chain E: H.29 5 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A, 1 interactions with chain E Hydrogen bonds: D:H.93, A:R.87 Water bridges: D:H.97, A:R.87, E:H.29

2 x NA: SODIUM ION(Non-functional Binders)

NA.7: 5 residues within 4Å: Chain B: S.22, K.25, N.27, A.30, Y.32 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.27, B:A.30 Water bridges: B:I.24 NA.18: 5 residues within 4Å: Chain E: S.22, K.25, N.27, A.30, Y.32 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:S.22, E:A.30 Water bridges: E:I.24

2 x K: POTASSIUM ION(Non-covalent)

K.8: 4 residues within 4Å: Chain A: H.22, D.32 Chain B: H.85, H.89 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Metal complexes: B:H.85, B:H.89, A:H.22, A:D.32 K.19: 4 residues within 4Å: Chain D: H.22, D.32 Chain E: H.85, H.89 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain D Metal complexes: E:H.85, E:H.89, D:H.22, D:D.32

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.9: 7 residues within 4Å: Chain B: Q.71, I.75 Chain E: Q.71, I.75 Ligands: PGE.4, PGE.15, EDO.20 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:Q.71, E:Q.71 EDO.20: 7 residues within 4Å: Chain B: Q.71, I.75 Chain E: Q.71, I.75 Ligands: PGE.4, EDO.9, PGE.15 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:Q.71, E:Q.71

2 x F3U: 4-methanoyl-2-(6-oxidanyl-3-oxidanylidene-4~{H}-xanthen-9-yl)benzoic acid(Covalent)

F3U.10: 3 residues within 4Å: Chain A: R.12 Chain C: R.1, S.2 2 PLIP interactions: 2 interactions with chain A pi-Cation interactions: A:R.12, A:R.12 F3U.21: 3 residues within 4Å: Chain D: R.12 Chain F: R.1, S.2 2 PLIP interactions: 2 interactions with chain D pi-Cation interactions: D:R.12, D:R.12

2 x NH2: AMINO GROUP(Non-functional Binders)

NH2.11: 2 residues within 4Å: Chain C: Y.16, G.18 No protein-ligand interaction detected (PLIP) NH2.22: 2 residues within 4Å: Chain F: Y.16, G.18 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Diaz-Perlas, C. et al., High-affinity peptides developed against calprotectin and their application as synthetic ligands in diagnostic assays. Nat Commun (2023)

Release Date

2023-02-01

Peptides

Protein S100-A9: AD
Protein S100-A8: BE
Peptide 3: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

D
B

B
A

E
A

C
C

F
C

Protein S100-A9

Protein S100-A8

Peptide 3