SMTL ID : 5yjg.1

Structural insights into periostin functions

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 3 residues within 4Å: Chain A: Y.450, F.565, N.571 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.564 Water bridges: A:R.451, A:E.566, A:N.571 NA.34: 3 residues within 4Å: Chain B: Y.450, F.565, N.571 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.564 Water bridges: B:R.451, B:E.566, B:N.571

2 x CYS: CYSTEINE(Non-covalent)

CYS.2: 4 residues within 4Å: Chain A: D.26, Q.27, C.48, Y.52 No protein-ligand interaction detected (PLIP) CYS.35: 4 residues within 4Å: Chain B: D.26, Q.27, C.48, Y.52 No protein-ligand interaction detected (PLIP)

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

CL.3: 1 residues within 4Å: Chain A: G.306 Ligand excluded by PLIP CL.4: 1 residues within 4Å: Chain A: G.380 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain A: K.580 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: E.66, C.67, R.73 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain A: R.111 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain A: T.47 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: R.161, A.206, G.209 Chain B: V.449 Ligand excluded by PLIP CL.10: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: N.189, M.304, G.305 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain A: K.490, Q.493 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain A: Y.450, R.451, A.453, V.454 Chain B: R.161 Ligand excluded by PLIP CL.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.15: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain A: K.54, S.55, K.60 Ligand excluded by PLIP CL.17: 1 residues within 4Å: Chain A: Q.410 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain B: N.429, Q.467 Ligand excluded by PLIP CL.36: 1 residues within 4Å: Chain B: G.306 Ligand excluded by PLIP CL.37: 1 residues within 4Å: Chain B: G.380 Ligand excluded by PLIP CL.38: 1 residues within 4Å: Chain B: K.580 Ligand excluded by PLIP CL.39: 3 residues within 4Å: Chain B: E.66, C.67, R.73 Ligand excluded by PLIP CL.40: 1 residues within 4Å: Chain B: R.111 Ligand excluded by PLIP CL.41: 1 residues within 4Å: Chain B: T.47 Ligand excluded by PLIP CL.42: 4 residues within 4Å: Chain A: V.449 Chain B: R.161, A.206, G.209 Ligand excluded by PLIP CL.43: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.44: 3 residues within 4Å: Chain B: N.189, M.304, G.305 Ligand excluded by PLIP CL.45: 2 residues within 4Å: Chain B: K.490, Q.493 Ligand excluded by PLIP CL.46: 5 residues within 4Å: Chain A: R.161 Chain B: Y.450, R.451, A.453, V.454 Ligand excluded by PLIP CL.47: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.48: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.49: 3 residues within 4Å: Chain B: K.54, S.55, K.60 Ligand excluded by PLIP CL.50: 1 residues within 4Å: Chain B: Q.410 Ligand excluded by PLIP CL.51: 2 residues within 4Å: Chain A: N.429, Q.467 Ligand excluded by PLIP

12 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.19: 2 residues within 4Å: Chain A: D.246, K.282 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.246 CA.20: 2 residues within 4Å: Chain A: G.366, K.367 No protein-ligand interaction detected (PLIP) CA.21: 3 residues within 4Å: Chain A: H.88, Y.90, G.91 No protein-ligand interaction detected (PLIP) CA.22: 3 residues within 4Å: Chain A: T.164, K.165, H.186 No protein-ligand interaction detected (PLIP) CA.23: 3 residues within 4Å: Chain A: N.433, Y.450, V.559 No protein-ligand interaction detected (PLIP) CA.24: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.52: 2 residues within 4Å: Chain B: D.246, K.282 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.246 CA.53: 2 residues within 4Å: Chain B: G.366, K.367 No protein-ligand interaction detected (PLIP) CA.54: 3 residues within 4Å: Chain B: H.88, Y.90, G.91 No protein-ligand interaction detected (PLIP) CA.55: 3 residues within 4Å: Chain B: T.164, K.165, H.186 No protein-ligand interaction detected (PLIP) CA.56: 3 residues within 4Å: Chain B: N.433, Y.450, V.559 No protein-ligand interaction detected (PLIP) CA.57: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

16 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.25: 8 residues within 4Å: Chain A: A.98, T.99, T.100, T.101, P.125, S.126, N.127, W.130 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:P.125 MG.26: 8 residues within 4Å: Chain A: D.234, L.235, S.237, F.238, P.262, T.263, N.264, F.267 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:P.262 MG.27: 8 residues within 4Å: Chain A: Q.368, Q.369, T.371, F.372, P.396, V.397, N.398, F.401 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:P.396 MG.28: 6 residues within 4Å: Chain A: F.497, T.499, F.500, P.524, N.526, F.529 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:F.497 MG.29: 6 residues within 4Å: Chain A: C.196, R.216, C.299, S.300, E.301, D.338 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.196, A:D.338 MG.30: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.31: 5 residues within 4Å: Chain A: G.562, E.585, L.590, S.600, D.601 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.600, A:D.601 MG.32: 8 residues within 4Å: Chain A: F.183, I.184, N.185, T.193, V.194, N.195, C.196, C.299 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:F.183 MG.58: 8 residues within 4Å: Chain B: A.98, T.99, T.100, T.101, P.125, S.126, N.127, W.130 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:P.125 MG.59: 8 residues within 4Å: Chain B: D.234, L.235, S.237, F.238, P.262, T.263, N.264, F.267 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:P.262 MG.60: 8 residues within 4Å: Chain B: Q.368, Q.369, T.371, F.372, P.396, V.397, N.398, F.401 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:P.396 MG.61: 6 residues within 4Å: Chain B: F.497, T.499, F.500, P.524, N.526, F.529 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:F.497 MG.62: 6 residues within 4Å: Chain B: C.196, R.216, C.299, S.300, E.301, D.338 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.196, B:D.338 MG.63: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.64: 5 residues within 4Å: Chain B: G.562, E.585, L.590, S.600, D.601 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.600, B:D.601 MG.65: 8 residues within 4Å: Chain B: F.183, I.184, N.185, T.193, V.194, N.195, C.196, C.299 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:F.183

2 x ZN: ZINC ION(Non-covalent)

ZN.33: 1 residues within 4Å: Chain A: K.574 No protein-ligand interaction detected (PLIP) ZN.66: 1 residues within 4Å: Chain B: K.574 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, J. et al., Structural characterizations of human periostin dimerization and cysteinylation. FEBS Lett. (2018)

Release Date

2018-05-23

Peptides

Periostin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Periostin