SMTL ID : 6j4m.1

Thermal treated soybean seed H-2 ferritin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-24-mer

Ligands

84 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 8 residues within 4Å: Chain A: D.162, E.165 Chain I: D.162, E.165 Chain Q: D.162, E.165 Ligands: MG.29, MG.57 5 PLIP interactions: 2 interactions with chain I, 1 interactions with chain Q, 2 interactions with chain A Metal complexes: I:D.162, I:E.165, Q:D.162, A:D.162, A:E.165 MG.2: 1 residues within 4Å: Chain A: D.42 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.42, A:D.42, H2O.1, H2O.1 MG.3: 5 residues within 4Å: Chain A: E.54, E.89, H.92, T.141, Q.172 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.54, A:E.89, A:H.92, H2O.1, H2O.1 MG.4: 3 residues within 4Å: Chain A: E.89, E.138, S.175 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.89, A:E.138, A:E.138, H2O.1, H2O.1 MG.5: 8 residues within 4Å: Chain B: D.162, E.165 Chain P: D.162, E.165 Chain V: D.162, E.165 Ligands: MG.54, MG.75 6 PLIP interactions: 2 interactions with chain P, 2 interactions with chain V, 2 interactions with chain B Metal complexes: P:D.162, P:E.165, V:D.162, V:E.165, B:D.162, B:E.165 MG.6: 5 residues within 4Å: Chain B: E.54, E.89, H.92, T.141, Q.172 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.54, B:E.89, B:H.92, H2O.2, H2O.3 MG.7: 3 residues within 4Å: Chain B: E.89, E.138, S.175 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.89, B:E.138, H2O.3 MG.8: 8 residues within 4Å: Chain C: D.162, E.165 Chain M: D.162, E.165 Chain W: D.162, E.165 Ligands: MG.43, MG.78 5 PLIP interactions: 1 interactions with chain W, 2 interactions with chain C, 2 interactions with chain M Metal complexes: W:D.162, C:D.162, C:E.165, M:D.162, M:E.165 MG.9: 1 residues within 4Å: Chain C: D.42 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.42, C:D.42, H2O.4, H2O.4 MG.10: 5 residues within 4Å: Chain C: E.54, E.89, H.92, T.141, Q.172 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.54, C:E.89, C:H.92, H2O.4, H2O.4 MG.11: 3 residues within 4Å: Chain C: E.89, E.138, S.175 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.89, C:E.138, C:E.138, H2O.4, H2O.4 MG.12: 8 residues within 4Å: Chain D: D.162, E.165 Chain L: D.162, E.165 Chain T: D.162, E.165 Ligands: MG.40, MG.68 6 PLIP interactions: 2 interactions with chain L, 2 interactions with chain T, 2 interactions with chain D Metal complexes: L:D.162, L:E.165, T:D.162, T:E.165, D:D.162, D:E.165 MG.13: 5 residues within 4Å: Chain D: E.54, E.89, H.92, T.141, Q.172 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.54, D:E.89, D:H.92, H2O.6, H2O.6 MG.14: 3 residues within 4Å: Chain D: E.89, E.138, S.175 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.89, D:E.138, H2O.6 MG.15: 8 residues within 4Å: Chain E: D.162, E.165 Chain O: D.162, E.165 Chain S: D.162, E.165 Ligands: MG.50, MG.64 5 PLIP interactions: 2 interactions with chain E, 1 interactions with chain S, 2 interactions with chain O Metal complexes: E:D.162, E:E.165, S:D.162, O:D.162, O:E.165 MG.16: 1 residues within 4Å: Chain E: D.42 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.42, E:D.42, H2O.7, H2O.7 MG.17: 5 residues within 4Å: Chain E: E.54, E.89, H.92, T.141, Q.172 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.54, E:E.89, E:H.92, H2O.7, H2O.7 MG.18: 3 residues within 4Å: Chain E: E.89, E.138, S.175 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.89, E:E.138, E:E.138, H2O.7, H2O.8 MG.19: 8 residues within 4Å: Chain F: D.162, E.165 Chain J: D.162, E.165 Chain X: D.162, E.165 Ligands: MG.33, MG.82 6 PLIP interactions: 2 interactions with chain F, 2 interactions with chain X, 2 interactions with chain J Metal complexes: F:D.162, F:E.165, X:D.162, X:E.165, J:D.162, J:E.165 MG.20: 5 residues within 4Å: Chain F: E.54, E.89, H.92, T.141, Q.172 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.54, F:E.89, F:H.92, H2O.9, H2O.9 MG.21: 3 residues within 4Å: Chain F: E.89, E.138, S.175 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.89, F:E.138, H2O.9 MG.22: 8 residues within 4Å: Chain G: D.162, E.165 Chain K: D.162, E.165 Chain U: D.162, E.165 Ligands: MG.36, MG.71 5 PLIP interactions: 2 interactions with chain G, 2 interactions with chain K, 1 interactions with chain U Metal complexes: G:D.162, G:E.165, K:D.162, K:E.165, U:D.162 MG.23: 1 residues within 4Å: Chain G: D.42 4 PLIP interactions: 2 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.42, G:D.42, H2O.10, H2O.10 MG.24: 5 residues within 4Å: Chain G: E.54, E.89, H.92, T.141, Q.172 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.54, G:E.89, G:H.92, H2O.10, H2O.11 MG.25: 3 residues within 4Å: Chain G: E.89, E.138, S.175 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.89, G:E.138, G:E.138, H2O.11, H2O.11 MG.26: 8 residues within 4Å: Chain H: D.162, E.165 Chain N: D.162, E.165 Chain R: D.162, E.165 Ligands: MG.47, MG.61 6 PLIP interactions: 2 interactions with chain H, 2 interactions with chain N, 2 interactions with chain R Metal complexes: H:D.162, H:E.165, N:D.162, N:E.165, R:D.162, R:E.165 MG.27: 5 residues within 4Å: Chain H: E.54, E.89, H.92, T.141, Q.172 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:E.54, H:E.89, H:H.92, H2O.12, H2O.12 MG.28: 3 residues within 4Å: Chain H: E.89, E.138, S.175 3 PLIP interactions: 2 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:E.89, H:E.138, H2O.12 MG.29: 8 residues within 4Å: Chain A: D.162, E.165 Chain I: D.162, E.165 Chain Q: D.162, E.165 Ligands: MG.1, MG.57 5 PLIP interactions: 1 interactions with chain Q, 2 interactions with chain A, 2 interactions with chain I Metal complexes: Q:D.162, A:D.162, A:E.165, I:D.162, I:E.165 MG.30: 1 residues within 4Å: Chain I: D.42 4 PLIP interactions: 2 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:D.42, I:D.42, H2O.13, H2O.13 MG.31: 5 residues within 4Å: Chain I: E.54, E.89, H.92, T.141, Q.172 5 PLIP interactions: 3 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:E.54, I:E.89, I:H.92, H2O.13, H2O.14 MG.32: 3 residues within 4Å: Chain I: E.89, E.138, S.175 5 PLIP interactions: 3 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:E.89, I:E.138, I:E.138, H2O.14, H2O.14 MG.33: 8 residues within 4Å: Chain F: D.162, E.165 Chain J: D.162, E.165 Chain X: D.162, E.165 Ligands: MG.19, MG.82 6 PLIP interactions: 2 interactions with chain J, 2 interactions with chain F, 2 interactions with chain X Metal complexes: J:D.162, J:E.165, F:D.162, F:E.165, X:D.162, X:E.165 MG.34: 5 residues within 4Å: Chain J: E.54, E.89, H.92, T.141, Q.172 5 PLIP interactions: 3 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:E.54, J:E.89, J:H.92, H2O.15, H2O.15 MG.35: 3 residues within 4Å: Chain J: E.89, E.138, S.175 3 PLIP interactions: 2 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:E.89, J:E.138, H2O.15 MG.36: 8 residues within 4Å: Chain G: D.162, E.165 Chain K: D.162, E.165 Chain U: D.162, E.165 Ligands: MG.22, MG.71 5 PLIP interactions: 2 interactions with chain K, 2 interactions with chain G, 1 interactions with chain U Metal complexes: K:D.162, K:E.165, G:D.162, G:E.165, U:D.162 MG.37: 1 residues within 4Å: Chain K: D.42 4 PLIP interactions: 2 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:D.42, K:D.42, H2O.16, H2O.16 MG.38: 5 residues within 4Å: Chain K: E.54, E.89, H.92, T.141, Q.172 5 PLIP interactions: 3 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:E.54, K:E.89, K:H.92, H2O.16, H2O.17 MG.39: 3 residues within 4Å: Chain K: E.89, E.138, S.175 5 PLIP interactions: 3 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:E.89, K:E.138, K:E.138, H2O.17, H2O.17 MG.40: 8 residues within 4Å: Chain D: D.162, E.165 Chain L: D.162, E.165 Chain T: D.162, E.165 Ligands: MG.12, MG.68 6 PLIP interactions: 2 interactions with chain L, 2 interactions with chain D, 2 interactions with chain T Metal complexes: L:D.162, L:E.165, D:D.162, D:E.165, T:D.162, T:E.165 MG.41: 5 residues within 4Å: Chain L: E.54, E.89, H.92, T.141, Q.172 5 PLIP interactions: 3 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:E.54, L:E.89, L:H.92, H2O.18, H2O.18 MG.42: 3 residues within 4Å: Chain L: E.89, E.138, S.175 3 PLIP interactions: 2 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:E.89, L:E.138, H2O.18 MG.43: 8 residues within 4Å: Chain C: D.162, E.165 Chain M: D.162, E.165 Chain W: D.162, E.165 Ligands: MG.8, MG.78 5 PLIP interactions: 2 interactions with chain C, 2 interactions with chain M, 1 interactions with chain W Metal complexes: C:D.162, C:E.165, M:D.162, M:E.165, W:D.162 MG.44: 1 residues within 4Å: Chain M: D.42 4 PLIP interactions: 2 interactions with chain M, 2 Ligand-Water interactions Metal complexes: M:D.42, M:D.42, H2O.19, H2O.20 MG.45: 5 residues within 4Å: Chain M: E.54, E.89, H.92, T.141, Q.172 5 PLIP interactions: 3 interactions with chain M, 2 Ligand-Water interactions Metal complexes: M:E.54, M:E.89, M:H.92, H2O.20, H2O.20 MG.46: 3 residues within 4Å: Chain M: E.89, E.138, S.175 5 PLIP interactions: 3 interactions with chain M, 2 Ligand-Water interactions Metal complexes: M:E.89, M:E.138, M:E.138, H2O.20, H2O.20 MG.47: 8 residues within 4Å: Chain H: D.162, E.165 Chain N: D.162, E.165 Chain R: D.162, E.165 Ligands: MG.26, MG.61 6 PLIP interactions: 2 interactions with chain R, 2 interactions with chain H, 2 interactions with chain N Metal complexes: R:D.162, R:E.165, H:D.162, H:E.165, N:D.162, N:E.165 MG.48: 5 residues within 4Å: Chain N: E.54, E.89, H.92, T.141, Q.172 5 PLIP interactions: 3 interactions with chain N, 2 Ligand-Water interactions Metal complexes: N:E.54, N:E.89, N:H.92, H2O.21, H2O.21 MG.49: 3 residues within 4Å: Chain N: E.89, E.138, S.175 3 PLIP interactions: 2 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:E.89, N:E.138, H2O.21 MG.50: 8 residues within 4Å: Chain E: D.162, E.165 Chain O: D.162, E.165 Chain S: D.162, E.165 Ligands: MG.15, MG.64 5 PLIP interactions: 2 interactions with chain E, 2 interactions with chain O, 1 interactions with chain S Metal complexes: E:D.162, E:E.165, O:D.162, O:E.165, S:D.162 MG.51: 1 residues within 4Å: Chain O: D.42 4 PLIP interactions: 2 interactions with chain O, 2 Ligand-Water interactions Metal complexes: O:D.42, O:D.42, H2O.22, H2O.23 MG.52: 5 residues within 4Å: Chain O: E.54, E.89, H.92, T.141, Q.172 5 PLIP interactions: 3 interactions with chain O, 2 Ligand-Water interactions Metal complexes: O:E.54, O:E.89, O:H.92, H2O.23, H2O.23 MG.53: 3 residues within 4Å: Chain O: E.89, E.138, S.175 5 PLIP interactions: 3 interactions with chain O, 2 Ligand-Water interactions Metal complexes: O:E.89, O:E.138, O:E.138, H2O.23, H2O.23 MG.54: 8 residues within 4Å: Chain B: D.162, E.165 Chain P: D.162, E.165 Chain V: D.162, E.165 Ligands: MG.5, MG.75 6 PLIP interactions: 2 interactions with chain V, 2 interactions with chain P, 2 interactions with chain B Metal complexes: V:D.162, V:E.165, P:D.162, P:E.165, B:D.162, B:E.165 MG.55: 5 residues within 4Å: Chain P: E.54, E.89, H.92, T.141, Q.172 5 PLIP interactions: 3 interactions with chain P, 2 Ligand-Water interactions Metal complexes: P:E.54, P:E.89, P:H.92, H2O.24, H2O.25 MG.56: 3 residues within 4Å: Chain P: E.89, E.138, S.175 3 PLIP interactions: 2 interactions with chain P, 1 Ligand-Water interactions Metal complexes: P:E.89, P:E.138, H2O.25 MG.57: 8 residues within 4Å: Chain A: D.162, E.165 Chain I: D.162, E.165 Chain Q: D.162, E.165 Ligands: MG.1, MG.29 5 PLIP interactions: 1 interactions with chain Q, 2 interactions with chain A, 2 interactions with chain I Metal complexes: Q:D.162, A:D.162, A:E.165, I:D.162, I:E.165 MG.58: 1 residues within 4Å: Chain Q: D.42 4 PLIP interactions: 2 interactions with chain Q, 2 Ligand-Water interactions Metal complexes: Q:D.42, Q:D.42, H2O.26, H2O.26 MG.59: 5 residues within 4Å: Chain Q: E.54, E.89, H.92, T.141, Q.172 5 PLIP interactions: 3 interactions with chain Q, 2 Ligand-Water interactions Metal complexes: Q:E.54, Q:E.89, Q:H.92, H2O.26, H2O.26 MG.60: 3 residues within 4Å: Chain Q: E.89, E.138, S.175 5 PLIP interactions: 3 interactions with chain Q, 2 Ligand-Water interactions Metal complexes: Q:E.89, Q:E.138, Q:E.138, H2O.26, H2O.26 MG.61: 8 residues within 4Å: Chain H: D.162, E.165 Chain N: D.162, E.165 Chain R: D.162, E.165 Ligands: MG.26, MG.47 6 PLIP interactions: 2 interactions with chain H, 2 interactions with chain N, 2 interactions with chain R Metal complexes: H:D.162, H:E.165, N:D.162, N:E.165, R:D.162, R:E.165 MG.62: 5 residues within 4Å: Chain R: E.54, E.89, H.92, T.141, Q.172 5 PLIP interactions: 3 interactions with chain R, 2 Ligand-Water interactions Metal complexes: R:E.54, R:E.89, R:H.92, H2O.27, H2O.28 MG.63: 3 residues within 4Å: Chain R: E.89, E.138, S.175 3 PLIP interactions: 2 interactions with chain R, 1 Ligand-Water interactions Metal complexes: R:E.89, R:E.138, H2O.28 MG.64: 8 residues within 4Å: Chain E: D.162, E.165 Chain O: D.162, E.165 Chain S: D.162, E.165 Ligands: MG.15, MG.50 5 PLIP interactions: 2 interactions with chain E, 1 interactions with chain S, 2 interactions with chain O Metal complexes: E:D.162, E:E.165, S:D.162, O:D.162, O:E.165 MG.65: 1 residues within 4Å: Chain S: D.42 4 PLIP interactions: 2 interactions with chain S, 2 Ligand-Water interactions Metal complexes: S:D.42, S:D.42, H2O.29, H2O.29 MG.66: 5 residues within 4Å: Chain S: E.54, E.89, H.92, T.141, Q.172 5 PLIP interactions: 3 interactions with chain S, 2 Ligand-Water interactions Metal complexes: S:E.54, S:E.89, S:H.92, H2O.29, H2O.29 MG.67: 3 residues within 4Å: Chain S: E.89, E.138, S.175 5 PLIP interactions: 3 interactions with chain S, 2 Ligand-Water interactions Metal complexes: S:E.89, S:E.138, S:E.138, H2O.29, H2O.29 MG.68: 8 residues within 4Å: Chain D: D.162, E.165 Chain L: D.162, E.165 Chain T: D.162, E.165 Ligands: MG.12, MG.40 6 PLIP interactions: 2 interactions with chain L, 2 interactions with chain T, 2 interactions with chain D Metal complexes: L:D.162, L:E.165, T:D.162, T:E.165, D:D.162, D:E.165 MG.69: 5 residues within 4Å: Chain T: E.54, E.89, H.92, T.141, Q.172 5 PLIP interactions: 3 interactions with chain T, 2 Ligand-Water interactions Metal complexes: T:E.54, T:E.89, T:H.92, H2O.30, H2O.31 MG.70: 3 residues within 4Å: Chain T: E.89, E.138, S.175 3 PLIP interactions: 2 interactions with chain T, 1 Ligand-Water interactions Metal complexes: T:E.89, T:E.138, H2O.31 MG.71: 8 residues within 4Å: Chain G: D.162, E.165 Chain K: D.162, E.165 Chain U: D.162, E.165 Ligands: MG.22, MG.36 5 PLIP interactions: 2 interactions with chain G, 1 interactions with chain U, 2 interactions with chain K Metal complexes: G:D.162, G:E.165, U:D.162, K:D.162, K:E.165 MG.72: 1 residues within 4Å: Chain U: D.42 4 PLIP interactions: 2 interactions with chain U, 2 Ligand-Water interactions Metal complexes: U:D.42, U:D.42, H2O.32, H2O.32 MG.73: 5 residues within 4Å: Chain U: E.54, E.89, H.92, T.141, Q.172 5 PLIP interactions: 3 interactions with chain U, 2 Ligand-Water interactions Metal complexes: U:E.54, U:E.89, U:H.92, H2O.32, H2O.32 MG.74: 3 residues within 4Å: Chain U: E.89, E.138, S.175 5 PLIP interactions: 3 interactions with chain U, 2 Ligand-Water interactions Metal complexes: U:E.89, U:E.138, U:E.138, H2O.32, H2O.33 MG.75: 8 residues within 4Å: Chain B: D.162, E.165 Chain P: D.162, E.165 Chain V: D.162, E.165 Ligands: MG.5, MG.54 6 PLIP interactions: 2 interactions with chain B, 2 interactions with chain V, 2 interactions with chain P Metal complexes: B:D.162, B:E.165, V:D.162, V:E.165, P:D.162, P:E.165 MG.76: 5 residues within 4Å: Chain V: E.54, E.89, H.92, T.141, Q.172 5 PLIP interactions: 3 interactions with chain V, 2 Ligand-Water interactions Metal complexes: V:E.54, V:E.89, V:H.92, H2O.34, H2O.34 MG.77: 3 residues within 4Å: Chain V: E.89, E.138, S.175 3 PLIP interactions: 2 interactions with chain V, 1 Ligand-Water interactions Metal complexes: V:E.89, V:E.138, H2O.34 MG.78: 8 residues within 4Å: Chain C: D.162, E.165 Chain M: D.162, E.165 Chain W: D.162, E.165 Ligands: MG.8, MG.43 5 PLIP interactions: 2 interactions with chain M, 2 interactions with chain C, 1 interactions with chain W Metal complexes: M:D.162, M:E.165, C:D.162, C:E.165, W:D.162 MG.79: 1 residues within 4Å: Chain W: D.42 4 PLIP interactions: 2 interactions with chain W, 2 Ligand-Water interactions Metal complexes: W:D.42, W:D.42, H2O.35, H2O.35 MG.80: 5 residues within 4Å: Chain W: E.54, E.89, H.92, T.141, Q.172 5 PLIP interactions: 3 interactions with chain W, 2 Ligand-Water interactions Metal complexes: W:E.54, W:E.89, W:H.92, H2O.35, H2O.36 MG.81: 3 residues within 4Å: Chain W: E.89, E.138, S.175 5 PLIP interactions: 3 interactions with chain W, 2 Ligand-Water interactions Metal complexes: W:E.89, W:E.138, W:E.138, H2O.36, H2O.36 MG.82: 8 residues within 4Å: Chain F: D.162, E.165 Chain J: D.162, E.165 Chain X: D.162, E.165 Ligands: MG.19, MG.33 6 PLIP interactions: 2 interactions with chain X, 2 interactions with chain F, 2 interactions with chain J Metal complexes: X:D.162, X:E.165, F:D.162, F:E.165, J:D.162, J:E.165 MG.83: 5 residues within 4Å: Chain X: E.54, E.89, H.92, T.141, Q.172 5 PLIP interactions: 3 interactions with chain X, 2 Ligand-Water interactions Metal complexes: X:E.54, X:E.89, X:H.92, H2O.37, H2O.37 MG.84: 3 residues within 4Å: Chain X: E.89, E.138, S.175 3 PLIP interactions: 2 interactions with chain X, 1 Ligand-Water interactions Metal complexes: X:E.89, X:E.138, H2O.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, X. et al., Thermostability of protein nanocages: the effect of natural extra peptide on the exterior surface. Rsc Adv (2019)

Release Date

2019-09-18

Peptides

Ferritin: ABCDEFGHIJKLMNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
A

C
H

D
A

E
H

F
A

G
H

H
A

I
H

J
A

K
H

L
A

M
H

N
A

O
H

P
A

Q
H

R
A

S
H

T
A

U
H

V
A

W
H

X
A

Ferritin

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