SMTL ID : 5yjh.1

Structural insights into periostin functions

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.96 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 2 residues within 4Å: Chain A: Y.448, N.569 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.569 NA.33: 2 residues within 4Å: Chain B: Y.448, N.569 No protein-ligand interaction detected (PLIP)

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

CL.2: 2 residues within 4Å: Chain A: K.52, S.53 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain A: T.45, K.47 Ligand excluded by PLIP CL.4: 1 residues within 4Å: Chain A: K.158 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain A: G.68 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: L.377, Q.408 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: L.426, Q.465, H.472 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: K.483, K.488, Q.491 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: E.64, C.65, R.71 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: N.187, M.302, G.303 Ligand excluded by PLIP CL.11: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain A: N.187 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain A: Y.448, R.449, V.452 Chain B: R.159 Ligand excluded by PLIP CL.14: 1 residues within 4Å: Chain A: K.365 Ligand excluded by PLIP CL.15: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain A: N.427, Q.465 Chain B: K.158 Ligand excluded by PLIP CL.17: 1 residues within 4Å: Chain A: K.578 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain A: L.36, Q.57 Ligand excluded by PLIP CL.19: 7 residues within 4Å: Chain A: S.117, R.159, T.205, N.206, G.207 Chain B: L.429, Y.430 Ligand excluded by PLIP CL.34: 2 residues within 4Å: Chain B: K.52, S.53 Ligand excluded by PLIP CL.35: 2 residues within 4Å: Chain B: T.45, K.47 Ligand excluded by PLIP CL.36: 1 residues within 4Å: Chain B: K.158 Ligand excluded by PLIP CL.37: 1 residues within 4Å: Chain B: G.68 Ligand excluded by PLIP CL.38: 2 residues within 4Å: Chain B: L.377, Q.408 Ligand excluded by PLIP CL.39: 3 residues within 4Å: Chain B: L.426, Q.465, H.472 Ligand excluded by PLIP CL.40: 3 residues within 4Å: Chain B: K.483, K.488, Q.491 Ligand excluded by PLIP CL.41: 3 residues within 4Å: Chain B: E.64, C.65, R.71 Ligand excluded by PLIP CL.42: 3 residues within 4Å: Chain B: N.187, M.302, G.303 Ligand excluded by PLIP CL.43: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.44: 1 residues within 4Å: Chain B: N.187 Ligand excluded by PLIP CL.45: 4 residues within 4Å: Chain A: R.159 Chain B: Y.448, R.449, V.452 Ligand excluded by PLIP CL.46: 1 residues within 4Å: Chain B: K.365 Ligand excluded by PLIP CL.47: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.48: 3 residues within 4Å: Chain A: K.158 Chain B: N.427, Q.465 Ligand excluded by PLIP CL.49: 1 residues within 4Å: Chain B: K.578 Ligand excluded by PLIP CL.50: 2 residues within 4Å: Chain B: L.36, Q.57 Ligand excluded by PLIP CL.51: 7 residues within 4Å: Chain A: L.429, Y.430 Chain B: S.117, R.159, T.205, N.206, G.207 Ligand excluded by PLIP

18 x MG: MAGNESIUM ION(Non-covalent)

MG.20: 6 residues within 4Å: Chain A: I.84, D.85, T.90, I.93, I.203, A.204 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.90, A:I.203 MG.21: 5 residues within 4Å: Chain A: R.444, G.515, D.516, V.557, T.603 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:G.515 MG.22: 7 residues within 4Å: Chain A: A.96, T.98, T.99, P.123, S.124, N.125, W.128 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:P.123 MG.23: 7 residues within 4Å: Chain A: D.232, L.233, S.235, F.236, P.260, T.261, F.265 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:P.260 MG.24: 9 residues within 4Å: Chain A: Q.366, Q.367, T.368, T.369, F.370, P.394, V.395, N.396, F.399 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:Q.366, A:P.394 MG.25: 7 residues within 4Å: Chain A: R.494, F.495, T.497, F.498, P.522, N.524, F.527 No protein-ligand interaction detected (PLIP) MG.26: 6 residues within 4Å: Chain A: C.194, R.214, C.297, S.298, E.299, D.336 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.194, A:D.336 MG.27: 5 residues within 4Å: Chain A: G.560, E.583, L.588, S.598, D.599 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.583, A:S.598, A:D.599 MG.28: 7 residues within 4Å: Chain A: F.181, N.183, T.191, V.192, N.193, C.194, C.297 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.191 MG.52: 6 residues within 4Å: Chain B: I.84, D.85, T.90, I.93, I.203, A.204 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.90, B:I.203 MG.53: 5 residues within 4Å: Chain B: R.444, G.515, D.516, V.557, T.603 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:G.515 MG.54: 7 residues within 4Å: Chain B: A.96, T.98, T.99, P.123, S.124, N.125, W.128 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:P.123 MG.55: 7 residues within 4Å: Chain B: D.232, L.233, S.235, F.236, P.260, T.261, F.265 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:P.260 MG.56: 9 residues within 4Å: Chain B: Q.366, Q.367, T.368, T.369, F.370, P.394, V.395, N.396, F.399 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:Q.366, B:P.394 MG.57: 7 residues within 4Å: Chain B: R.494, F.495, T.497, F.498, P.522, N.524, F.527 No protein-ligand interaction detected (PLIP) MG.58: 6 residues within 4Å: Chain B: C.194, R.214, C.297, S.298, E.299, D.336 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.194, B:D.336 MG.59: 5 residues within 4Å: Chain B: G.560, E.583, L.588, S.598, D.599 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.583, B:S.598, B:D.599 MG.60: 7 residues within 4Å: Chain B: F.181, N.183, T.191, V.192, N.193, C.194, C.297 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.191

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

CA.29: 1 residues within 4Å: Chain A: T.162 No protein-ligand interaction detected (PLIP) CA.30: 2 residues within 4Å: Chain A: N.431, V.557 No protein-ligand interaction detected (PLIP) CA.31: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.61: 1 residues within 4Å: Chain B: T.162 No protein-ligand interaction detected (PLIP) CA.62: 2 residues within 4Å: Chain B: N.431, V.557 No protein-ligand interaction detected (PLIP) CA.63: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.32: 1 residues within 4Å: Chain A: K.572 No protein-ligand interaction detected (PLIP) ZN.64: 1 residues within 4Å: Chain B: K.572 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