SMTL ID : 9jgp.1

Structure of Pd ions bound to human heavy chain ferritin nanocage.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

homo-24-mer

Ligands

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

NA.1: 4 residues within 4Å: Chain A: R.9, Q.10, N.11, Y.12 Ligand excluded by PLIP NA.2: 3 residues within 4Å: Chain A: Q.75 Chain E: N.139, K.143 Ligand excluded by PLIP NA.3: 3 residues within 4Å: Chain E: N.139, E.140, K.143 Ligand excluded by PLIP NA.4: 2 residues within 4Å: Chain A: H.13, Q.14 Ligand excluded by PLIP NA.11: 4 residues within 4Å: Chain B: R.9, Q.10, N.11, Y.12 Ligand excluded by PLIP NA.12: 3 residues within 4Å: Chain B: Q.75 Chain G: N.139, K.143 Ligand excluded by PLIP NA.13: 3 residues within 4Å: Chain G: N.139, E.140, K.143 Ligand excluded by PLIP NA.14: 2 residues within 4Å: Chain B: H.13, Q.14 Ligand excluded by PLIP NA.21: 4 residues within 4Å: Chain C: R.9, Q.10, N.11, Y.12 Ligand excluded by PLIP NA.22: 3 residues within 4Å: Chain C: Q.75 Chain H: N.139, K.143 Ligand excluded by PLIP NA.23: 3 residues within 4Å: Chain H: N.139, E.140, K.143 Ligand excluded by PLIP NA.24: 2 residues within 4Å: Chain C: H.13, Q.14 Ligand excluded by PLIP NA.31: 4 residues within 4Å: Chain D: R.9, Q.10, N.11, Y.12 Ligand excluded by PLIP NA.32: 3 residues within 4Å: Chain D: Q.75 Chain F: N.139, K.143 Ligand excluded by PLIP NA.33: 3 residues within 4Å: Chain F: N.139, E.140, K.143 Ligand excluded by PLIP NA.34: 2 residues within 4Å: Chain D: H.13, Q.14 Ligand excluded by PLIP NA.41: 4 residues within 4Å: Chain E: R.9, Q.10, N.11, Y.12 Ligand excluded by PLIP NA.42: 3 residues within 4Å: Chain E: Q.75 Chain I: N.139, K.143 Ligand excluded by PLIP NA.43: 3 residues within 4Å: Chain I: N.139, E.140, K.143 Ligand excluded by PLIP NA.44: 2 residues within 4Å: Chain E: H.13, Q.14 Ligand excluded by PLIP NA.51: 4 residues within 4Å: Chain F: R.9, Q.10, N.11, Y.12 Ligand excluded by PLIP NA.52: 3 residues within 4Å: Chain F: Q.75 Chain K: N.139, K.143 Ligand excluded by PLIP NA.53: 3 residues within 4Å: Chain K: N.139, E.140, K.143 Ligand excluded by PLIP NA.54: 2 residues within 4Å: Chain F: H.13, Q.14 Ligand excluded by PLIP NA.61: 4 residues within 4Å: Chain G: R.9, Q.10, N.11, Y.12 Ligand excluded by PLIP NA.62: 3 residues within 4Å: Chain G: Q.75 Chain L: N.139, K.143 Ligand excluded by PLIP NA.63: 3 residues within 4Å: Chain L: N.139, E.140, K.143 Ligand excluded by PLIP NA.64: 2 residues within 4Å: Chain G: H.13, Q.14 Ligand excluded by PLIP NA.71: 4 residues within 4Å: Chain H: R.9, Q.10, N.11, Y.12 Ligand excluded by PLIP NA.72: 3 residues within 4Å: Chain H: Q.75 Chain J: N.139, K.143 Ligand excluded by PLIP NA.73: 3 residues within 4Å: Chain J: N.139, E.140, K.143 Ligand excluded by PLIP NA.74: 2 residues within 4Å: Chain H: H.13, Q.14 Ligand excluded by PLIP NA.81: 4 residues within 4Å: Chain I: R.9, Q.10, N.11, Y.12 Ligand excluded by PLIP NA.82: 3 residues within 4Å: Chain A: N.139, K.143 Chain I: Q.75 Ligand excluded by PLIP NA.83: 3 residues within 4Å: Chain A: N.139, E.140, K.143 Ligand excluded by PLIP NA.84: 2 residues within 4Å: Chain I: H.13, Q.14 Ligand excluded by PLIP NA.91: 4 residues within 4Å: Chain J: R.9, Q.10, N.11, Y.12 Ligand excluded by PLIP NA.92: 3 residues within 4Å: Chain C: N.139, K.143 Chain J: Q.75 Ligand excluded by PLIP NA.93: 3 residues within 4Å: Chain C: N.139, E.140, K.143 Ligand excluded by PLIP NA.94: 2 residues within 4Å: Chain J: H.13, Q.14 Ligand excluded by PLIP NA.101: 4 residues within 4Å: Chain K: R.9, Q.10, N.11, Y.12 Ligand excluded by PLIP NA.102: 3 residues within 4Å: Chain D: N.139, K.143 Chain K: Q.75 Ligand excluded by PLIP NA.103: 3 residues within 4Å: Chain D: N.139, E.140, K.143 Ligand excluded by PLIP NA.104: 2 residues within 4Å: Chain K: H.13, Q.14 Ligand excluded by PLIP NA.111: 4 residues within 4Å: Chain L: R.9, Q.10, N.11, Y.12 Ligand excluded by PLIP NA.112: 3 residues within 4Å: Chain B: N.139, K.143 Chain L: Q.75 Ligand excluded by PLIP NA.113: 3 residues within 4Å: Chain B: N.139, E.140, K.143 Ligand excluded by PLIP NA.114: 2 residues within 4Å: Chain L: H.13, Q.14 Ligand excluded by PLIP NA.121: 4 residues within 4Å: Chain M: R.9, Q.10, N.11, Y.12 Ligand excluded by PLIP NA.122: 3 residues within 4Å: Chain M: Q.75 Chain Q: N.139, K.143 Ligand excluded by PLIP NA.123: 3 residues within 4Å: Chain Q: N.139, E.140, K.143 Ligand excluded by PLIP NA.124: 2 residues within 4Å: Chain M: H.13, Q.14 Ligand excluded by PLIP NA.131: 4 residues within 4Å: Chain N: R.9, Q.10, N.11, Y.12 Ligand excluded by PLIP NA.132: 3 residues within 4Å: Chain N: Q.75 Chain S: N.139, K.143 Ligand excluded by PLIP NA.133: 3 residues within 4Å: Chain S: N.139, E.140, K.143 Ligand excluded by PLIP NA.134: 2 residues within 4Å: Chain N: H.13, Q.14 Ligand excluded by PLIP NA.141: 4 residues within 4Å: Chain O: R.9, Q.10, N.11, Y.12 Ligand excluded by PLIP NA.142: 3 residues within 4Å: Chain O: Q.75 Chain T: N.139, K.143 Ligand excluded by PLIP NA.143: 3 residues within 4Å: Chain T: N.139, E.140, K.143 Ligand excluded by PLIP NA.144: 2 residues within 4Å: Chain O: H.13, Q.14 Ligand excluded by PLIP NA.151: 4 residues within 4Å: Chain P: R.9, Q.10, N.11, Y.12 Ligand excluded by PLIP NA.152: 3 residues within 4Å: Chain P: Q.75 Chain R: N.139, K.143 Ligand excluded by PLIP NA.153: 3 residues within 4Å: Chain R: N.139, E.140, K.143 Ligand excluded by PLIP NA.154: 2 residues within 4Å: Chain P: H.13, Q.14 Ligand excluded by PLIP NA.161: 4 residues within 4Å: Chain Q: R.9, Q.10, N.11, Y.12 Ligand excluded by PLIP NA.162: 3 residues within 4Å: Chain Q: Q.75 Chain U: N.139, K.143 Ligand excluded by PLIP NA.163: 3 residues within 4Å: Chain U: N.139, E.140, K.143 Ligand excluded by PLIP NA.164: 2 residues within 4Å: Chain Q: H.13, Q.14 Ligand excluded by PLIP NA.171: 4 residues within 4Å: Chain R: R.9, Q.10, N.11, Y.12 Ligand excluded by PLIP NA.172: 3 residues within 4Å: Chain R: Q.75 Chain W: N.139, K.143 Ligand excluded by PLIP NA.173: 3 residues within 4Å: Chain W: N.139, E.140, K.143 Ligand excluded by PLIP NA.174: 2 residues within 4Å: Chain R: H.13, Q.14 Ligand excluded by PLIP NA.181: 4 residues within 4Å: Chain S: R.9, Q.10, N.11, Y.12 Ligand excluded by PLIP NA.182: 3 residues within 4Å: Chain S: Q.75 Chain X: N.139, K.143 Ligand excluded by PLIP NA.183: 3 residues within 4Å: Chain X: N.139, E.140, K.143 Ligand excluded by PLIP NA.184: 2 residues within 4Å: Chain S: H.13, Q.14 Ligand excluded by PLIP NA.191: 4 residues within 4Å: Chain T: R.9, Q.10, N.11, Y.12 Ligand excluded by PLIP NA.192: 3 residues within 4Å: Chain T: Q.75 Chain V: N.139, K.143 Ligand excluded by PLIP NA.193: 3 residues within 4Å: Chain V: N.139, E.140, K.143 Ligand excluded by PLIP NA.194: 2 residues within 4Å: Chain T: H.13, Q.14 Ligand excluded by PLIP NA.201: 4 residues within 4Å: Chain U: R.9, Q.10, N.11, Y.12 Ligand excluded by PLIP NA.202: 3 residues within 4Å: Chain M: N.139, K.143 Chain U: Q.75 Ligand excluded by PLIP NA.203: 3 residues within 4Å: Chain M: N.139, E.140, K.143 Ligand excluded by PLIP NA.204: 2 residues within 4Å: Chain U: H.13, Q.14 Ligand excluded by PLIP NA.211: 4 residues within 4Å: Chain V: R.9, Q.10, N.11, Y.12 Ligand excluded by PLIP NA.212: 3 residues within 4Å: Chain O: N.139, K.143 Chain V: Q.75 Ligand excluded by PLIP NA.213: 3 residues within 4Å: Chain O: N.139, E.140, K.143 Ligand excluded by PLIP NA.214: 2 residues within 4Å: Chain V: H.13, Q.14 Ligand excluded by PLIP NA.221: 4 residues within 4Å: Chain W: R.9, Q.10, N.11, Y.12 Ligand excluded by PLIP NA.222: 3 residues within 4Å: Chain P: N.139, K.143 Chain W: Q.75 Ligand excluded by PLIP NA.223: 3 residues within 4Å: Chain P: N.139, E.140, K.143 Ligand excluded by PLIP NA.224: 2 residues within 4Å: Chain W: H.13, Q.14 Ligand excluded by PLIP NA.231: 4 residues within 4Å: Chain X: R.9, Q.10, N.11, Y.12 Ligand excluded by PLIP NA.232: 3 residues within 4Å: Chain N: N.139, K.143 Chain X: Q.75 Ligand excluded by PLIP NA.233: 3 residues within 4Å: Chain N: N.139, E.140, K.143 Ligand excluded by PLIP NA.234: 2 residues within 4Å: Chain X: H.13, Q.14 Ligand excluded by PLIP

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

MG.5: 3 residues within 4Å: Chain A: E.27, E.62, H.65 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.27, A:E.62, A:H.65, H2O.1, H2O.2 MG.6: 5 residues within 4Å: Chain A: E.134 Chain E: E.134 Chain I: E.134 Ligands: MG.46, MG.86 No protein-ligand interaction detected (PLIP) MG.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain B: E.27, E.62, H.65 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.27, B:E.62, B:H.65, H2O.7, H2O.8 MG.16: 5 residues within 4Å: Chain B: E.134 Chain G: E.134 Chain L: E.134 Ligands: MG.66, MG.116 No protein-ligand interaction detected (PLIP) MG.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.25: 3 residues within 4Å: Chain C: E.27, E.62, H.65 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.27, C:E.62, C:H.65, H2O.14, H2O.15 MG.26: 5 residues within 4Å: Chain C: E.134 Chain H: E.134 Chain J: E.134 Ligands: MG.76, MG.96 No protein-ligand interaction detected (PLIP) MG.27: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.28: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.35: 3 residues within 4Å: Chain D: E.27, E.62, H.65 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.27, D:E.62, D:H.65, H2O.20, H2O.21 MG.36: 5 residues within 4Å: Chain D: E.134 Chain F: E.134 Chain K: E.134 Ligands: MG.56, MG.106 No protein-ligand interaction detected (PLIP) MG.37: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.38: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.45: 3 residues within 4Å: Chain E: E.27, E.62, H.65 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.27, E:E.62, E:H.65, H2O.27, H2O.28 MG.46: 5 residues within 4Å: Chain A: E.134 Chain E: E.134 Chain I: E.134 Ligands: MG.6, MG.86 No protein-ligand interaction detected (PLIP) MG.47: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.48: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.55: 3 residues within 4Å: Chain F: E.27, E.62, H.65 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.27, F:E.62, F:H.65, H2O.33, H2O.34 MG.56: 5 residues within 4Å: Chain D: E.134 Chain F: E.134 Chain K: E.134 Ligands: MG.36, MG.106 No protein-ligand interaction detected (PLIP) MG.57: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.58: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.65: 3 residues within 4Å: Chain G: E.27, E.62, H.65 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.27, G:E.62, G:H.65, H2O.40, H2O.41 MG.66: 5 residues within 4Å: Chain B: E.134 Chain G: E.134 Chain L: E.134 Ligands: MG.16, MG.116 No protein-ligand interaction detected (PLIP) MG.67: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.68: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.75: 3 residues within 4Å: Chain H: E.27, E.62, H.65 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:E.27, H:E.62, H:H.65, H2O.46, H2O.47 MG.76: 5 residues within 4Å: Chain C: E.134 Chain H: E.134 Chain J: E.134 Ligands: MG.26, MG.96 No protein-ligand interaction detected (PLIP) MG.77: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.78: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.85: 3 residues within 4Å: Chain I: E.27, E.62, H.65 5 PLIP interactions: 3 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:E.27, I:E.62, I:H.65, H2O.53, H2O.54 MG.86: 5 residues within 4Å: Chain A: E.134 Chain E: E.134 Chain I: E.134 Ligands: MG.6, MG.46 No protein-ligand interaction detected (PLIP) MG.87: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.88: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.95: 3 residues within 4Å: Chain J: E.27, E.62, H.65 5 PLIP interactions: 3 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:E.27, J:E.62, J:H.65, H2O.59, H2O.60 MG.96: 5 residues within 4Å: Chain C: E.134 Chain H: E.134 Chain J: E.134 Ligands: MG.26, MG.76 No protein-ligand interaction detected (PLIP) MG.97: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.98: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.105: 3 residues within 4Å: Chain K: E.27, E.62, H.65 5 PLIP interactions: 3 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:E.27, K:E.62, K:H.65, H2O.65, H2O.67 MG.106: 5 residues within 4Å: Chain D: E.134 Chain F: E.134 Chain K: E.134 Ligands: MG.36, MG.56 No protein-ligand interaction detected (PLIP) MG.107: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.108: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.115: 3 residues within 4Å: Chain L: E.27, E.62, H.65 5 PLIP interactions: 3 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:E.27, L:E.62, L:H.65, H2O.72, H2O.73 MG.116: 5 residues within 4Å: Chain B: E.134 Chain G: E.134 Chain L: E.134 Ligands: MG.16, MG.66 No protein-ligand interaction detected (PLIP) MG.117: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.118: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.125: 3 residues within 4Å: Chain M: E.27, E.62, H.65 5 PLIP interactions: 3 interactions with chain M, 2 Ligand-Water interactions Metal complexes: M:E.27, M:E.62, M:H.65, H2O.78, H2O.79 MG.126: 5 residues within 4Å: Chain M: E.134 Chain Q: E.134 Chain U: E.134 Ligands: MG.166, MG.206 No protein-ligand interaction detected (PLIP) MG.127: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.128: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.135: 3 residues within 4Å: Chain N: E.27, E.62, H.65 5 PLIP interactions: 3 interactions with chain N, 2 Ligand-Water interactions Metal complexes: N:E.27, N:E.62, N:H.65, H2O.85, H2O.86 MG.136: 5 residues within 4Å: Chain N: E.134 Chain S: E.134 Chain X: E.134 Ligands: MG.186, MG.236 No protein-ligand interaction detected (PLIP) MG.137: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.138: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.145: 3 residues within 4Å: Chain O: E.27, E.62, H.65 5 PLIP interactions: 3 interactions with chain O, 2 Ligand-Water interactions Metal complexes: O:E.27, O:E.62, O:H.65, H2O.91, H2O.92 MG.146: 5 residues within 4Å: Chain O: E.134 Chain T: E.134 Chain V: E.134 Ligands: MG.196, MG.216 No protein-ligand interaction detected (PLIP) MG.147: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.148: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.155: 3 residues within 4Å: Chain P: E.27, E.62, H.65 5 PLIP interactions: 3 interactions with chain P, 2 Ligand-Water interactions Metal complexes: P:E.27, P:E.62, P:H.65, H2O.98, H2O.99 MG.156: 5 residues within 4Å: Chain P: E.134 Chain R: E.134 Chain W: E.134 Ligands: MG.176, MG.226 No protein-ligand interaction detected (PLIP) MG.157: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.158: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.165: 3 residues within 4Å: Chain Q: E.27, E.62, H.65 5 PLIP interactions: 3 interactions with chain Q, 2 Ligand-Water interactions Metal complexes: Q:E.27, Q:E.62, Q:H.65, H2O.104, H2O.105 MG.166: 5 residues within 4Å: Chain M: E.134 Chain Q: E.134 Chain U: E.134 Ligands: MG.126, MG.206 No protein-ligand interaction detected (PLIP) MG.167: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.168: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.175: 3 residues within 4Å: Chain R: E.27, E.62, H.65 5 PLIP interactions: 3 interactions with chain R, 2 Ligand-Water interactions Metal complexes: R:E.27, R:E.62, R:H.65, H2O.111, H2O.112 MG.176: 5 residues within 4Å: Chain P: E.134 Chain R: E.134 Chain W: E.134 Ligands: MG.156, MG.226 No protein-ligand interaction detected (PLIP) MG.177: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.178: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.185: 3 residues within 4Å: Chain S: E.27, E.62, H.65 5 PLIP interactions: 3 interactions with chain S, 2 Ligand-Water interactions Metal complexes: S:E.27, S:E.62, S:H.65, H2O.117, H2O.118 MG.186: 5 residues within 4Å: Chain N: E.134 Chain S: E.134 Chain X: E.134 Ligands: MG.136, MG.236 No protein-ligand interaction detected (PLIP) MG.187: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.188: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.195: 3 residues within 4Å: Chain T: E.27, E.62, H.65 5 PLIP interactions: 3 interactions with chain T, 2 Ligand-Water interactions Metal complexes: T:E.27, T:E.62, T:H.65, H2O.124, H2O.125 MG.196: 5 residues within 4Å: Chain O: E.134 Chain T: E.134 Chain V: E.134 Ligands: MG.146, MG.216 No protein-ligand interaction detected (PLIP) MG.197: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.198: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.205: 3 residues within 4Å: Chain U: E.27, E.62, H.65 5 PLIP interactions: 3 interactions with chain U, 2 Ligand-Water interactions Metal complexes: U:E.27, U:E.62, U:H.65, H2O.130, H2O.131 MG.206: 5 residues within 4Å: Chain M: E.134 Chain Q: E.134 Chain U: E.134 Ligands: MG.126, MG.166 No protein-ligand interaction detected (PLIP) MG.207: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.208: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.215: 3 residues within 4Å: Chain V: E.27, E.62, H.65 5 PLIP interactions: 3 interactions with chain V, 2 Ligand-Water interactions Metal complexes: V:E.27, V:E.62, V:H.65, H2O.137, H2O.138 MG.216: 5 residues within 4Å: Chain O: E.134 Chain T: E.134 Chain V: E.134 Ligands: MG.146, MG.196 No protein-ligand interaction detected (PLIP) MG.217: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.218: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.225: 3 residues within 4Å: Chain W: E.27, E.62, H.65 5 PLIP interactions: 3 interactions with chain W, 2 Ligand-Water interactions Metal complexes: W:E.27, W:E.62, W:H.65, H2O.143, H2O.144 MG.226: 5 residues within 4Å: Chain P: E.134 Chain R: E.134 Chain W: E.134 Ligands: MG.156, MG.176 No protein-ligand interaction detected (PLIP) MG.227: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.228: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.235: 3 residues within 4Å: Chain X: E.27, E.62, H.65 5 PLIP interactions: 3 interactions with chain X, 2 Ligand-Water interactions Metal complexes: X:E.27, X:E.62, X:H.65, H2O.149, H2O.151 MG.236: 5 residues within 4Å: Chain N: E.134 Chain S: E.134 Chain X: E.134 Ligands: MG.136, MG.186 No protein-ligand interaction detected (PLIP) MG.237: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.238: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

48 x PD: PALLADIUM ION(Non-covalent)

PD.9: 2 residues within 4Å: Chain A: H.13, K.124 Ligand excluded by PLIP PD.10: 11 residues within 4Å: Chain A: L.169, H.173 Chain B: L.169, H.173 Chain O: L.169, H.173 Chain P: L.169, H.173 Ligands: PD.20, PD.150, PD.160 Ligand excluded by PLIP PD.19: 2 residues within 4Å: Chain B: H.13, K.124 Ligand excluded by PLIP PD.20: 11 residues within 4Å: Chain A: L.169, H.173 Chain B: L.169, H.173 Chain O: L.169, H.173 Chain P: L.169, H.173 Ligands: PD.10, PD.150, PD.160 Ligand excluded by PLIP PD.29: 2 residues within 4Å: Chain C: H.13, K.124 Ligand excluded by PLIP PD.30: 11 residues within 4Å: Chain C: L.169, H.173 Chain D: L.169, H.173 Chain M: L.169, H.173 Chain N: L.169, H.173 Ligands: PD.40, PD.130, PD.140 Ligand excluded by PLIP PD.39: 2 residues within 4Å: Chain D: H.13, K.124 Ligand excluded by PLIP PD.40: 11 residues within 4Å: Chain C: L.169, H.173 Chain D: L.169, H.173 Chain M: L.169, H.173 Chain N: L.169, H.173 Ligands: PD.30, PD.130, PD.140 Ligand excluded by PLIP PD.49: 2 residues within 4Å: Chain E: H.13, K.124 Ligand excluded by PLIP PD.50: 11 residues within 4Å: Chain E: L.169, H.173 Chain F: L.169, H.173 Chain U: L.169, H.173 Chain V: L.169, H.173 Ligands: PD.60, PD.210, PD.220 Ligand excluded by PLIP PD.59: 2 residues within 4Å: Chain F: H.13, K.124 Ligand excluded by PLIP PD.60: 11 residues within 4Å: Chain E: L.169, H.173 Chain F: L.169, H.173 Chain U: L.169, H.173 Chain V: L.169, H.173 Ligands: PD.50, PD.210, PD.220 Ligand excluded by PLIP PD.69: 2 residues within 4Å: Chain G: H.13, K.124 Ligand excluded by PLIP PD.70: 11 residues within 4Å: Chain G: L.169, H.173 Chain H: L.169, H.173 Chain W: L.169, H.173 Chain X: L.169, H.173 Ligands: PD.80, PD.230, PD.240 Ligand excluded by PLIP PD.79: 2 residues within 4Å: Chain H: H.13, K.124 Ligand excluded by PLIP PD.80: 11 residues within 4Å: Chain G: L.169, H.173 Chain H: L.169, H.173 Chain W: L.169, H.173 Chain X: L.169, H.173 Ligands: PD.70, PD.230, PD.240 Ligand excluded by PLIP PD.89: 2 residues within 4Å: Chain I: H.13, K.124 Ligand excluded by PLIP PD.90: 11 residues within 4Å: Chain I: L.169, H.173 Chain J: L.169, H.173 Chain Q: L.169, H.173 Chain R: L.169, H.173 Ligands: PD.100, PD.170, PD.180 Ligand excluded by PLIP PD.99: 2 residues within 4Å: Chain J: H.13, K.124 Ligand excluded by PLIP PD.100: 11 residues within 4Å: Chain I: L.169, H.173 Chain J: L.169, H.173 Chain Q: L.169, H.173 Chain R: L.169, H.173 Ligands: PD.90, PD.170, PD.180 Ligand excluded by PLIP PD.109: 2 residues within 4Å: Chain K: H.13, K.124 Ligand excluded by PLIP PD.110: 11 residues within 4Å: Chain K: L.169, H.173 Chain L: L.169, H.173 Chain S: L.169, H.173 Chain T: L.169, H.173 Ligands: PD.120, PD.190, PD.200 Ligand excluded by PLIP PD.119: 2 residues within 4Å: Chain L: H.13, K.124 Ligand excluded by PLIP PD.120: 11 residues within 4Å: Chain K: L.169, H.173 Chain L: L.169, H.173 Chain S: L.169, H.173 Chain T: L.169, H.173 Ligands: PD.110, PD.190, PD.200 Ligand excluded by PLIP PD.129: 2 residues within 4Å: Chain M: H.13, K.124 Ligand excluded by PLIP PD.130: 11 residues within 4Å: Chain C: L.169, H.173 Chain D: L.169, H.173 Chain M: L.169, H.173 Chain N: L.169, H.173 Ligands: PD.30, PD.40, PD.140 Ligand excluded by PLIP PD.139: 2 residues within 4Å: Chain N: H.13, K.124 Ligand excluded by PLIP PD.140: 11 residues within 4Å: Chain C: L.169, H.173 Chain D: L.169, H.173 Chain M: L.169, H.173 Chain N: L.169, H.173 Ligands: PD.30, PD.40, PD.130 Ligand excluded by PLIP PD.149: 2 residues within 4Å: Chain O: H.13, K.124 Ligand excluded by PLIP PD.150: 11 residues within 4Å: Chain A: L.169, H.173 Chain B: L.169, H.173 Chain O: L.169, H.173 Chain P: L.169, H.173 Ligands: PD.10, PD.20, PD.160 Ligand excluded by PLIP PD.159: 2 residues within 4Å: Chain P: H.13, K.124 Ligand excluded by PLIP PD.160: 11 residues within 4Å: Chain A: L.169, H.173 Chain B: L.169, H.173 Chain O: L.169, H.173 Chain P: L.169, H.173 Ligands: PD.10, PD.20, PD.150 Ligand excluded by PLIP PD.169: 2 residues within 4Å: Chain Q: H.13, K.124 Ligand excluded by PLIP PD.170: 11 residues within 4Å: Chain I: L.169, H.173 Chain J: L.169, H.173 Chain Q: L.169, H.173 Chain R: L.169, H.173 Ligands: PD.90, PD.100, PD.180 Ligand excluded by PLIP PD.179: 2 residues within 4Å: Chain R: H.13, K.124 Ligand excluded by PLIP PD.180: 11 residues within 4Å: Chain I: L.169, H.173 Chain J: L.169, H.173 Chain Q: L.169, H.173 Chain R: L.169, H.173 Ligands: PD.90, PD.100, PD.170 Ligand excluded by PLIP PD.189: 2 residues within 4Å: Chain S: H.13, K.124 Ligand excluded by PLIP PD.190: 11 residues within 4Å: Chain K: L.169, H.173 Chain L: L.169, H.173 Chain S: L.169, H.173 Chain T: L.169, H.173 Ligands: PD.110, PD.120, PD.200 Ligand excluded by PLIP PD.199: 2 residues within 4Å: Chain T: H.13, K.124 Ligand excluded by PLIP PD.200: 11 residues within 4Å: Chain K: L.169, H.173 Chain L: L.169, H.173 Chain S: L.169, H.173 Chain T: L.169, H.173 Ligands: PD.110, PD.120, PD.190 Ligand excluded by PLIP PD.209: 2 residues within 4Å: Chain U: H.13, K.124 Ligand excluded by PLIP PD.210: 11 residues within 4Å: Chain E: L.169, H.173 Chain F: L.169, H.173 Chain U: L.169, H.173 Chain V: L.169, H.173 Ligands: PD.50, PD.60, PD.220 Ligand excluded by PLIP PD.219: 2 residues within 4Å: Chain V: H.13, K.124 Ligand excluded by PLIP PD.220: 11 residues within 4Å: Chain E: L.169, H.173 Chain F: L.169, H.173 Chain U: L.169, H.173 Chain V: L.169, H.173 Ligands: PD.50, PD.60, PD.210 Ligand excluded by PLIP PD.229: 2 residues within 4Å: Chain W: H.13, K.124 Ligand excluded by PLIP PD.230: 11 residues within 4Å: Chain G: L.169, H.173 Chain H: L.169, H.173 Chain W: L.169, H.173 Chain X: L.169, H.173 Ligands: PD.70, PD.80, PD.240 Ligand excluded by PLIP PD.239: 2 residues within 4Å: Chain X: H.13, K.124 Ligand excluded by PLIP PD.240: 11 residues within 4Å: Chain G: L.169, H.173 Chain H: L.169, H.173 Chain W: L.169, H.173 Chain X: L.169, H.173 Ligands: PD.70, PD.80, PD.230 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hu, X.Y. et al., Structure of Pd ions bound to human heavy chain ferritin nanocage. To Be Published

Release Date

2025-09-10

Peptides

Ferritin heavy chain, N-terminally processed: ABCDEFGHIJKLMNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

I
A

J
A

K
A

L
A

M
A

N
A

O
A

P
A

Q
A

R
A

S
A

T
A

U
A

V
A

W
A

X
A

Ferritin heavy chain, N-terminally processed