SMTL ID : 6lru.1

Marsupenaeus japonicus ferritin mutant (T158H)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-24-mer

Ligands

48 x IMD: IMIDAZOLE(Non-covalent)(Non-functional Binders)

IMD.1: 10 residues within 4Å: Chain A: Y.31, F.51, S.55, E.58, E.59, H.62, E.104, S.141, I.145 Ligands: NI.4 Ligand excluded by PLIP IMD.5: 1 residues within 4Å: Ligands: NI.3 Ligand excluded by PLIP IMD.6: 10 residues within 4Å: Chain B: Y.31, F.51, S.55, E.58, E.59, H.62, E.104, S.141, I.145 Ligands: NI.9 Ligand excluded by PLIP IMD.10: 1 residues within 4Å: Ligands: NI.8 Ligand excluded by PLIP IMD.11: 10 residues within 4Å: Chain C: Y.31, F.51, S.55, E.58, E.59, H.62, E.104, S.141, I.145 Ligands: NI.14 Ligand excluded by PLIP IMD.15: 1 residues within 4Å: Ligands: NI.13 Ligand excluded by PLIP IMD.16: 10 residues within 4Å: Chain D: Y.31, F.51, S.55, E.58, E.59, H.62, E.104, S.141, I.145 Ligands: NI.19 Ligand excluded by PLIP IMD.20: 1 residues within 4Å: Ligands: NI.18 Ligand excluded by PLIP IMD.21: 10 residues within 4Å: Chain E: Y.31, F.51, S.55, E.58, E.59, H.62, E.104, S.141, I.145 Ligands: NI.24 Ligand excluded by PLIP IMD.25: 1 residues within 4Å: Ligands: NI.23 Ligand excluded by PLIP IMD.26: 10 residues within 4Å: Chain F: Y.31, F.51, S.55, E.58, E.59, H.62, E.104, S.141, I.145 Ligands: NI.29 Ligand excluded by PLIP IMD.30: 1 residues within 4Å: Ligands: NI.28 Ligand excluded by PLIP IMD.31: 10 residues within 4Å: Chain G: Y.31, F.51, S.55, E.58, E.59, H.62, E.104, S.141, I.145 Ligands: NI.34 Ligand excluded by PLIP IMD.35: 1 residues within 4Å: Ligands: NI.33 Ligand excluded by PLIP IMD.36: 10 residues within 4Å: Chain H: Y.31, F.51, S.55, E.58, E.59, H.62, E.104, S.141, I.145 Ligands: NI.39 Ligand excluded by PLIP IMD.40: 1 residues within 4Å: Ligands: NI.38 Ligand excluded by PLIP IMD.41: 10 residues within 4Å: Chain I: Y.31, F.51, S.55, E.58, E.59, H.62, E.104, S.141, I.145 Ligands: NI.44 Ligand excluded by PLIP IMD.45: 1 residues within 4Å: Ligands: NI.43 Ligand excluded by PLIP IMD.46: 10 residues within 4Å: Chain J: Y.31, F.51, S.55, E.58, E.59, H.62, E.104, S.141, I.145 Ligands: NI.49 Ligand excluded by PLIP IMD.50: 1 residues within 4Å: Ligands: NI.48 Ligand excluded by PLIP IMD.51: 10 residues within 4Å: Chain K: Y.31, F.51, S.55, E.58, E.59, H.62, E.104, S.141, I.145 Ligands: NI.54 Ligand excluded by PLIP IMD.55: 1 residues within 4Å: Ligands: NI.53 Ligand excluded by PLIP IMD.56: 10 residues within 4Å: Chain L: Y.31, F.51, S.55, E.58, E.59, H.62, E.104, S.141, I.145 Ligands: NI.59 Ligand excluded by PLIP IMD.60: 1 residues within 4Å: Ligands: NI.58 Ligand excluded by PLIP IMD.61: 10 residues within 4Å: Chain M: Y.31, F.51, S.55, E.58, E.59, H.62, E.104, S.141, I.145 Ligands: NI.64 Ligand excluded by PLIP IMD.65: 1 residues within 4Å: Ligands: NI.63 Ligand excluded by PLIP IMD.66: 10 residues within 4Å: Chain N: Y.31, F.51, S.55, E.58, E.59, H.62, E.104, S.141, I.145 Ligands: NI.69 Ligand excluded by PLIP IMD.70: 1 residues within 4Å: Ligands: NI.68 Ligand excluded by PLIP IMD.71: 10 residues within 4Å: Chain O: Y.31, F.51, S.55, E.58, E.59, H.62, E.104, S.141, I.145 Ligands: NI.74 Ligand excluded by PLIP IMD.75: 1 residues within 4Å: Ligands: NI.73 Ligand excluded by PLIP IMD.76: 10 residues within 4Å: Chain P: Y.31, F.51, S.55, E.58, E.59, H.62, E.104, S.141, I.145 Ligands: NI.79 Ligand excluded by PLIP IMD.80: 1 residues within 4Å: Ligands: NI.78 Ligand excluded by PLIP IMD.81: 10 residues within 4Å: Chain Q: Y.31, F.51, S.55, E.58, E.59, H.62, E.104, S.141, I.145 Ligands: NI.84 Ligand excluded by PLIP IMD.85: 1 residues within 4Å: Ligands: NI.83 Ligand excluded by PLIP IMD.86: 10 residues within 4Å: Chain R: Y.31, F.51, S.55, E.58, E.59, H.62, E.104, S.141, I.145 Ligands: NI.89 Ligand excluded by PLIP IMD.90: 1 residues within 4Å: Ligands: NI.88 Ligand excluded by PLIP IMD.91: 10 residues within 4Å: Chain S: Y.31, F.51, S.55, E.58, E.59, H.62, E.104, S.141, I.145 Ligands: NI.94 Ligand excluded by PLIP IMD.95: 1 residues within 4Å: Ligands: NI.93 Ligand excluded by PLIP IMD.96: 10 residues within 4Å: Chain T: Y.31, F.51, S.55, E.58, E.59, H.62, E.104, S.141, I.145 Ligands: NI.99 Ligand excluded by PLIP IMD.100: 1 residues within 4Å: Ligands: NI.98 Ligand excluded by PLIP IMD.101: 10 residues within 4Å: Chain U: Y.31, F.51, S.55, E.58, E.59, H.62, E.104, S.141, I.145 Ligands: NI.104 Ligand excluded by PLIP IMD.105: 1 residues within 4Å: Ligands: NI.103 Ligand excluded by PLIP IMD.106: 10 residues within 4Å: Chain V: Y.31, F.51, S.55, E.58, E.59, H.62, E.104, S.141, I.145 Ligands: NI.109 Ligand excluded by PLIP IMD.110: 1 residues within 4Å: Ligands: NI.108 Ligand excluded by PLIP IMD.111: 10 residues within 4Å: Chain W: Y.31, F.51, S.55, E.58, E.59, H.62, E.104, S.141, I.145 Ligands: NI.114 Ligand excluded by PLIP IMD.115: 1 residues within 4Å: Ligands: NI.113 Ligand excluded by PLIP IMD.116: 10 residues within 4Å: Chain X: Y.31, F.51, S.55, E.58, E.59, H.62, E.104, S.141, I.145 Ligands: NI.119 Ligand excluded by PLIP IMD.120: 1 residues within 4Å: Ligands: NI.118 Ligand excluded by PLIP

24 x FE: FE (III) ION(Non-covalent)

FE.2: 4 residues within 4Å: Chain A: E.24, E.59, H.62, V.107 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.24, A:E.59, A:H.62, H2O.1, H2O.2 FE.7: 4 residues within 4Å: Chain B: E.24, E.59, H.62, V.107 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.24, B:E.59, B:H.62, H2O.9, H2O.9 FE.12: 4 residues within 4Å: Chain C: E.24, E.59, H.62, V.107 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.24, C:E.59, C:H.62, H2O.16, H2O.16 FE.17: 4 residues within 4Å: Chain D: E.24, E.59, H.62, V.107 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.24, D:E.59, D:H.62, H2O.23, H2O.24 FE.22: 4 residues within 4Å: Chain E: E.24, E.59, H.62, V.107 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.24, E:E.59, E:H.62, H2O.31, H2O.31 FE.27: 4 residues within 4Å: Chain F: E.24, E.59, H.62, V.107 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.24, F:E.59, F:H.62, H2O.38, H2O.38 FE.32: 4 residues within 4Å: Chain G: E.24, E.59, H.62, V.107 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.24, G:E.59, G:H.62, H2O.45, H2O.46 FE.37: 4 residues within 4Å: Chain H: E.24, E.59, H.62, V.107 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:E.24, H:E.59, H:H.62, H2O.52, H2O.53 FE.42: 4 residues within 4Å: Chain I: E.24, E.59, H.62, V.107 5 PLIP interactions: 3 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:E.24, I:E.59, I:H.62, H2O.60, H2O.60 FE.47: 4 residues within 4Å: Chain J: E.24, E.59, H.62, V.107 5 PLIP interactions: 3 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:E.24, J:E.59, J:H.62, H2O.67, H2O.67 FE.52: 4 residues within 4Å: Chain K: E.24, E.59, H.62, V.107 5 PLIP interactions: 3 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:E.24, K:E.59, K:H.62, H2O.74, H2O.75 FE.57: 4 residues within 4Å: Chain L: E.24, E.59, H.62, V.107 5 PLIP interactions: 3 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:E.24, L:E.59, L:H.62, H2O.82, H2O.82 FE.62: 4 residues within 4Å: Chain M: E.24, E.59, H.62, V.107 5 PLIP interactions: 3 interactions with chain M, 2 Ligand-Water interactions Metal complexes: M:E.24, M:E.59, M:H.62, H2O.89, H2O.89 FE.67: 4 residues within 4Å: Chain N: E.24, E.59, H.62, V.107 5 PLIP interactions: 3 interactions with chain N, 2 Ligand-Water interactions Metal complexes: N:E.24, N:E.59, N:H.62, H2O.96, H2O.97 FE.72: 4 residues within 4Å: Chain O: E.24, E.59, H.62, V.107 5 PLIP interactions: 3 interactions with chain O, 2 Ligand-Water interactions Metal complexes: O:E.24, O:E.59, O:H.62, H2O.104, H2O.104 FE.77: 4 residues within 4Å: Chain P: E.24, E.59, H.62, V.107 5 PLIP interactions: 3 interactions with chain P, 2 Ligand-Water interactions Metal complexes: P:E.24, P:E.59, P:H.62, H2O.111, H2O.111 FE.82: 4 residues within 4Å: Chain Q: E.24, E.59, H.62, V.107 5 PLIP interactions: 3 interactions with chain Q, 2 Ligand-Water interactions Metal complexes: Q:E.24, Q:E.59, Q:H.62, H2O.118, H2O.119 FE.87: 4 residues within 4Å: Chain R: E.24, E.59, H.62, V.107 5 PLIP interactions: 3 interactions with chain R, 2 Ligand-Water interactions Metal complexes: R:E.24, R:E.59, R:H.62, H2O.126, H2O.126 FE.92: 4 residues within 4Å: Chain S: E.24, E.59, H.62, V.107 5 PLIP interactions: 3 interactions with chain S, 2 Ligand-Water interactions Metal complexes: S:E.24, S:E.59, S:H.62, H2O.133, H2O.133 FE.97: 4 residues within 4Å: Chain T: E.24, E.59, H.62, V.107 5 PLIP interactions: 3 interactions with chain T, 2 Ligand-Water interactions Metal complexes: T:E.24, T:E.59, T:H.62, H2O.140, H2O.141 FE.102: 4 residues within 4Å: Chain U: E.24, E.59, H.62, V.107 5 PLIP interactions: 3 interactions with chain U, 2 Ligand-Water interactions Metal complexes: U:E.24, U:E.59, U:H.62, H2O.147, H2O.148 FE.107: 4 residues within 4Å: Chain V: E.24, E.59, H.62, V.107 5 PLIP interactions: 3 interactions with chain V, 2 Ligand-Water interactions Metal complexes: V:E.24, V:E.59, V:H.62, H2O.155, H2O.155 FE.112: 4 residues within 4Å: Chain W: E.24, E.59, H.62, V.107 5 PLIP interactions: 3 interactions with chain W, 2 Ligand-Water interactions Metal complexes: W:E.24, W:E.59, W:H.62, H2O.162, H2O.162 FE.117: 4 residues within 4Å: Chain X: E.24, E.59, H.62, V.107 5 PLIP interactions: 3 interactions with chain X, 2 Ligand-Water interactions Metal complexes: X:E.24, X:E.59, X:H.62, H2O.169, H2O.170

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

NI.3: 2 residues within 4Å: Chain A: E.95 Ligands: IMD.5 Ligand excluded by PLIP NI.4: 5 residues within 4Å: Chain A: S.55, E.58, S.141, K.144 Ligands: IMD.1 Ligand excluded by PLIP NI.8: 2 residues within 4Å: Chain B: E.95 Ligands: IMD.10 Ligand excluded by PLIP NI.9: 5 residues within 4Å: Chain B: S.55, E.58, S.141, K.144 Ligands: IMD.6 Ligand excluded by PLIP NI.13: 2 residues within 4Å: Chain C: E.95 Ligands: IMD.15 Ligand excluded by PLIP NI.14: 5 residues within 4Å: Chain C: S.55, E.58, S.141, K.144 Ligands: IMD.11 Ligand excluded by PLIP NI.18: 2 residues within 4Å: Chain D: E.95 Ligands: IMD.20 Ligand excluded by PLIP NI.19: 5 residues within 4Å: Chain D: S.55, E.58, S.141, K.144 Ligands: IMD.16 Ligand excluded by PLIP NI.23: 2 residues within 4Å: Chain E: E.95 Ligands: IMD.25 Ligand excluded by PLIP NI.24: 5 residues within 4Å: Chain E: S.55, E.58, S.141, K.144 Ligands: IMD.21 Ligand excluded by PLIP NI.28: 2 residues within 4Å: Chain F: E.95 Ligands: IMD.30 Ligand excluded by PLIP NI.29: 5 residues within 4Å: Chain F: S.55, E.58, S.141, K.144 Ligands: IMD.26 Ligand excluded by PLIP NI.33: 2 residues within 4Å: Chain G: E.95 Ligands: IMD.35 Ligand excluded by PLIP NI.34: 5 residues within 4Å: Chain G: S.55, E.58, S.141, K.144 Ligands: IMD.31 Ligand excluded by PLIP NI.38: 2 residues within 4Å: Chain H: E.95 Ligands: IMD.40 Ligand excluded by PLIP NI.39: 5 residues within 4Å: Chain H: S.55, E.58, S.141, K.144 Ligands: IMD.36 Ligand excluded by PLIP NI.43: 2 residues within 4Å: Chain I: E.95 Ligands: IMD.45 Ligand excluded by PLIP NI.44: 5 residues within 4Å: Chain I: S.55, E.58, S.141, K.144 Ligands: IMD.41 Ligand excluded by PLIP NI.48: 2 residues within 4Å: Chain J: E.95 Ligands: IMD.50 Ligand excluded by PLIP NI.49: 5 residues within 4Å: Chain J: S.55, E.58, S.141, K.144 Ligands: IMD.46 Ligand excluded by PLIP NI.53: 2 residues within 4Å: Chain K: E.95 Ligands: IMD.55 Ligand excluded by PLIP NI.54: 5 residues within 4Å: Chain K: S.55, E.58, S.141, K.144 Ligands: IMD.51 Ligand excluded by PLIP NI.58: 2 residues within 4Å: Chain L: E.95 Ligands: IMD.60 Ligand excluded by PLIP NI.59: 5 residues within 4Å: Chain L: S.55, E.58, S.141, K.144 Ligands: IMD.56 Ligand excluded by PLIP NI.63: 2 residues within 4Å: Chain M: E.95 Ligands: IMD.65 Ligand excluded by PLIP NI.64: 5 residues within 4Å: Chain M: S.55, E.58, S.141, K.144 Ligands: IMD.61 Ligand excluded by PLIP NI.68: 2 residues within 4Å: Chain N: E.95 Ligands: IMD.70 Ligand excluded by PLIP NI.69: 5 residues within 4Å: Chain N: S.55, E.58, S.141, K.144 Ligands: IMD.66 Ligand excluded by PLIP NI.73: 2 residues within 4Å: Chain O: E.95 Ligands: IMD.75 Ligand excluded by PLIP NI.74: 5 residues within 4Å: Chain O: S.55, E.58, S.141, K.144 Ligands: IMD.71 Ligand excluded by PLIP NI.78: 2 residues within 4Å: Chain P: E.95 Ligands: IMD.80 Ligand excluded by PLIP NI.79: 5 residues within 4Å: Chain P: S.55, E.58, S.141, K.144 Ligands: IMD.76 Ligand excluded by PLIP NI.83: 2 residues within 4Å: Chain Q: E.95 Ligands: IMD.85 Ligand excluded by PLIP NI.84: 5 residues within 4Å: Chain Q: S.55, E.58, S.141, K.144 Ligands: IMD.81 Ligand excluded by PLIP NI.88: 2 residues within 4Å: Chain R: E.95 Ligands: IMD.90 Ligand excluded by PLIP NI.89: 5 residues within 4Å: Chain R: S.55, E.58, S.141, K.144 Ligands: IMD.86 Ligand excluded by PLIP NI.93: 2 residues within 4Å: Chain S: E.95 Ligands: IMD.95 Ligand excluded by PLIP NI.94: 5 residues within 4Å: Chain S: S.55, E.58, S.141, K.144 Ligands: IMD.91 Ligand excluded by PLIP NI.98: 2 residues within 4Å: Chain T: E.95 Ligands: IMD.100 Ligand excluded by PLIP NI.99: 5 residues within 4Å: Chain T: S.55, E.58, S.141, K.144 Ligands: IMD.96 Ligand excluded by PLIP NI.103: 2 residues within 4Å: Chain U: E.95 Ligands: IMD.105 Ligand excluded by PLIP NI.104: 5 residues within 4Å: Chain U: S.55, E.58, S.141, K.144 Ligands: IMD.101 Ligand excluded by PLIP NI.108: 2 residues within 4Å: Chain V: E.95 Ligands: IMD.110 Ligand excluded by PLIP NI.109: 5 residues within 4Å: Chain V: S.55, E.58, S.141, K.144 Ligands: IMD.106 Ligand excluded by PLIP NI.113: 2 residues within 4Å: Chain W: E.95 Ligands: IMD.115 Ligand excluded by PLIP NI.114: 5 residues within 4Å: Chain W: S.55, E.58, S.141, K.144 Ligands: IMD.111 Ligand excluded by PLIP NI.118: 2 residues within 4Å: Chain X: E.95 Ligands: IMD.120 Ligand excluded by PLIP NI.119: 5 residues within 4Å: Chain X: S.55, E.58, S.141, K.144 Ligands: IMD.116 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tan, X. et al., Converting histidine-induced 3D protein arrays in crystals into their 3D analogues in solution by metal coordination cross-linking. Commun Chem (2020)

Release Date

2020-11-25

Peptides

Ferritin: 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

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