SMTL ID : 6tr9.1

Crystal structure of human L ferritin (HuLf) triple variant E60A-E61A-E64A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.46 Å

Oligo State

homo-24-mer

Ligands

168 x CD: CADMIUM ION(Non-covalent)(Non-functional Binders)

CD.1: 5 residues within 4Å: Chain A: D.128 Chain H: D.128 Chain K: D.128 Ligands: CD.50, CD.71 Ligand excluded by PLIP CD.2: 8 residues within 4Å: Chain A: C.127, D.128, E.131 Chain H: E.131 Chain K: E.131 Ligands: CD.3, CD.51, CD.72 Ligand excluded by PLIP CD.3: 5 residues within 4Å: Chain A: H.115, S.119, C.127, E.131 Ligands: CD.2 Ligand excluded by PLIP CD.4: 2 residues within 4Å: Chain A: D.12, R.121 Ligand excluded by PLIP CD.5: 2 residues within 4Å: Chain A: H.133 Chain K: D.136 Ligand excluded by PLIP CD.6: 1 residues within 4Å: Chain A: E.46 Ligand excluded by PLIP CD.7: 3 residues within 4Å: Chain A: E.87, D.95, A.99 Ligand excluded by PLIP CD.8: 5 residues within 4Å: Chain B: D.128 Chain F: D.128 Chain J: D.128 Ligands: CD.36, CD.64 Ligand excluded by PLIP CD.9: 8 residues within 4Å: Chain B: C.127, D.128, E.131 Chain F: E.131 Chain J: E.131 Ligands: CD.10, CD.37, CD.65 Ligand excluded by PLIP CD.10: 5 residues within 4Å: Chain B: H.115, S.119, C.127, E.131 Ligands: CD.9 Ligand excluded by PLIP CD.11: 2 residues within 4Å: Chain B: D.12, R.121 Ligand excluded by PLIP CD.12: 2 residues within 4Å: Chain B: H.133 Chain J: D.136 Ligand excluded by PLIP CD.13: 1 residues within 4Å: Chain B: E.46 Ligand excluded by PLIP CD.14: 3 residues within 4Å: Chain B: E.87, D.95, A.99 Ligand excluded by PLIP CD.15: 5 residues within 4Å: Chain C: D.128 Chain E: D.128 Chain L: D.128 Ligands: CD.29, CD.78 Ligand excluded by PLIP CD.16: 8 residues within 4Å: Chain C: C.127, D.128, E.131 Chain E: E.131 Chain L: E.131 Ligands: CD.17, CD.30, CD.79 Ligand excluded by PLIP CD.17: 5 residues within 4Å: Chain C: H.115, S.119, C.127, E.131 Ligands: CD.16 Ligand excluded by PLIP CD.18: 2 residues within 4Å: Chain C: D.12, R.121 Ligand excluded by PLIP CD.19: 2 residues within 4Å: Chain C: H.133 Chain L: D.136 Ligand excluded by PLIP CD.20: 1 residues within 4Å: Chain C: E.46 Ligand excluded by PLIP CD.21: 3 residues within 4Å: Chain C: E.87, D.95, A.99 Ligand excluded by PLIP CD.22: 5 residues within 4Å: Chain D: D.128 Chain G: D.128 Chain I: D.128 Ligands: CD.43, CD.57 Ligand excluded by PLIP CD.23: 8 residues within 4Å: Chain D: C.127, D.128, E.131 Chain G: E.131 Chain I: E.131 Ligands: CD.24, CD.44, CD.58 Ligand excluded by PLIP CD.24: 5 residues within 4Å: Chain D: H.115, S.119, C.127, E.131 Ligands: CD.23 Ligand excluded by PLIP CD.25: 2 residues within 4Å: Chain D: D.12, R.121 Ligand excluded by PLIP CD.26: 2 residues within 4Å: Chain D: H.133 Chain I: D.136 Ligand excluded by PLIP CD.27: 1 residues within 4Å: Chain D: E.46 Ligand excluded by PLIP CD.28: 3 residues within 4Å: Chain D: E.87, D.95, A.99 Ligand excluded by PLIP CD.29: 5 residues within 4Å: Chain C: D.128 Chain E: D.128 Chain L: D.128 Ligands: CD.15, CD.78 Ligand excluded by PLIP CD.30: 8 residues within 4Å: Chain C: E.131 Chain E: C.127, D.128, E.131 Chain L: E.131 Ligands: CD.16, CD.31, CD.79 Ligand excluded by PLIP CD.31: 5 residues within 4Å: Chain E: H.115, S.119, C.127, E.131 Ligands: CD.30 Ligand excluded by PLIP CD.32: 2 residues within 4Å: Chain E: D.12, R.121 Ligand excluded by PLIP CD.33: 2 residues within 4Å: Chain C: D.136 Chain E: H.133 Ligand excluded by PLIP CD.34: 1 residues within 4Å: Chain E: E.46 Ligand excluded by PLIP CD.35: 3 residues within 4Å: Chain E: E.87, D.95, A.99 Ligand excluded by PLIP CD.36: 5 residues within 4Å: Chain B: D.128 Chain F: D.128 Chain J: D.128 Ligands: CD.8, CD.64 Ligand excluded by PLIP CD.37: 8 residues within 4Å: Chain B: E.131 Chain F: C.127, D.128, E.131 Chain J: E.131 Ligands: CD.9, CD.38, CD.65 Ligand excluded by PLIP CD.38: 5 residues within 4Å: Chain F: H.115, S.119, C.127, E.131 Ligands: CD.37 Ligand excluded by PLIP CD.39: 2 residues within 4Å: Chain F: D.12, R.121 Ligand excluded by PLIP CD.40: 2 residues within 4Å: Chain B: D.136 Chain F: H.133 Ligand excluded by PLIP CD.41: 1 residues within 4Å: Chain F: E.46 Ligand excluded by PLIP CD.42: 3 residues within 4Å: Chain F: E.87, D.95, A.99 Ligand excluded by PLIP CD.43: 5 residues within 4Å: Chain D: D.128 Chain G: D.128 Chain I: D.128 Ligands: CD.22, CD.57 Ligand excluded by PLIP CD.44: 8 residues within 4Å: Chain D: E.131 Chain G: C.127, D.128, E.131 Chain I: E.131 Ligands: CD.23, CD.45, CD.58 Ligand excluded by PLIP CD.45: 5 residues within 4Å: Chain G: H.115, S.119, C.127, E.131 Ligands: CD.44 Ligand excluded by PLIP CD.46: 2 residues within 4Å: Chain G: D.12, R.121 Ligand excluded by PLIP CD.47: 2 residues within 4Å: Chain D: D.136 Chain G: H.133 Ligand excluded by PLIP CD.48: 1 residues within 4Å: Chain G: E.46 Ligand excluded by PLIP CD.49: 3 residues within 4Å: Chain G: E.87, D.95, A.99 Ligand excluded by PLIP CD.50: 5 residues within 4Å: Chain A: D.128 Chain H: D.128 Chain K: D.128 Ligands: CD.1, CD.71 Ligand excluded by PLIP CD.51: 8 residues within 4Å: Chain A: E.131 Chain H: C.127, D.128, E.131 Chain K: E.131 Ligands: CD.2, CD.52, CD.72 Ligand excluded by PLIP CD.52: 5 residues within 4Å: Chain H: H.115, S.119, C.127, E.131 Ligands: CD.51 Ligand excluded by PLIP CD.53: 2 residues within 4Å: Chain H: D.12, R.121 Ligand excluded by PLIP CD.54: 2 residues within 4Å: Chain A: D.136 Chain H: H.133 Ligand excluded by PLIP CD.55: 1 residues within 4Å: Chain H: E.46 Ligand excluded by PLIP CD.56: 3 residues within 4Å: Chain H: E.87, D.95, A.99 Ligand excluded by PLIP CD.57: 5 residues within 4Å: Chain D: D.128 Chain G: D.128 Chain I: D.128 Ligands: CD.22, CD.43 Ligand excluded by PLIP CD.58: 8 residues within 4Å: Chain D: E.131 Chain G: E.131 Chain I: C.127, D.128, E.131 Ligands: CD.23, CD.44, CD.59 Ligand excluded by PLIP CD.59: 5 residues within 4Å: Chain I: H.115, S.119, C.127, E.131 Ligands: CD.58 Ligand excluded by PLIP CD.60: 2 residues within 4Å: Chain I: D.12, R.121 Ligand excluded by PLIP CD.61: 2 residues within 4Å: Chain G: D.136 Chain I: H.133 Ligand excluded by PLIP CD.62: 1 residues within 4Å: Chain I: E.46 Ligand excluded by PLIP CD.63: 3 residues within 4Å: Chain I: E.87, D.95, A.99 Ligand excluded by PLIP CD.64: 5 residues within 4Å: Chain B: D.128 Chain F: D.128 Chain J: D.128 Ligands: CD.8, CD.36 Ligand excluded by PLIP CD.65: 8 residues within 4Å: Chain B: E.131 Chain F: E.131 Chain J: C.127, D.128, E.131 Ligands: CD.9, CD.37, CD.66 Ligand excluded by PLIP CD.66: 5 residues within 4Å: Chain J: H.115, S.119, C.127, E.131 Ligands: CD.65 Ligand excluded by PLIP CD.67: 2 residues within 4Å: Chain J: D.12, R.121 Ligand excluded by PLIP CD.68: 2 residues within 4Å: Chain F: D.136 Chain J: H.133 Ligand excluded by PLIP CD.69: 1 residues within 4Å: Chain J: E.46 Ligand excluded by PLIP CD.70: 3 residues within 4Å: Chain J: E.87, D.95, A.99 Ligand excluded by PLIP CD.71: 5 residues within 4Å: Chain A: D.128 Chain H: D.128 Chain K: D.128 Ligands: CD.1, CD.50 Ligand excluded by PLIP CD.72: 8 residues within 4Å: Chain A: E.131 Chain H: E.131 Chain K: C.127, D.128, E.131 Ligands: CD.2, CD.51, CD.73 Ligand excluded by PLIP CD.73: 5 residues within 4Å: Chain K: H.115, S.119, C.127, E.131 Ligands: CD.72 Ligand excluded by PLIP CD.74: 2 residues within 4Å: Chain K: D.12, R.121 Ligand excluded by PLIP CD.75: 2 residues within 4Å: Chain H: D.136 Chain K: H.133 Ligand excluded by PLIP CD.76: 1 residues within 4Å: Chain K: E.46 Ligand excluded by PLIP CD.77: 3 residues within 4Å: Chain K: E.87, D.95, A.99 Ligand excluded by PLIP CD.78: 5 residues within 4Å: Chain C: D.128 Chain E: D.128 Chain L: D.128 Ligands: CD.15, CD.29 Ligand excluded by PLIP CD.79: 8 residues within 4Å: Chain C: E.131 Chain E: E.131 Chain L: C.127, D.128, E.131 Ligands: CD.16, CD.30, CD.80 Ligand excluded by PLIP CD.80: 5 residues within 4Å: Chain L: H.115, S.119, C.127, E.131 Ligands: CD.79 Ligand excluded by PLIP CD.81: 2 residues within 4Å: Chain L: D.12, R.121 Ligand excluded by PLIP CD.82: 2 residues within 4Å: Chain E: D.136 Chain L: H.133 Ligand excluded by PLIP CD.83: 1 residues within 4Å: Chain L: E.46 Ligand excluded by PLIP CD.84: 3 residues within 4Å: Chain L: E.87, D.95, A.99 Ligand excluded by PLIP CD.85: 5 residues within 4Å: Chain M: D.128 Chain T: D.128 Chain W: D.128 Ligands: CD.134, CD.155 Ligand excluded by PLIP CD.86: 8 residues within 4Å: Chain M: C.127, D.128, E.131 Chain T: E.131 Chain W: E.131 Ligands: CD.87, CD.135, CD.156 Ligand excluded by PLIP CD.87: 5 residues within 4Å: Chain M: H.115, S.119, C.127, E.131 Ligands: CD.86 Ligand excluded by PLIP CD.88: 2 residues within 4Å: Chain M: D.12, R.121 Ligand excluded by PLIP CD.89: 2 residues within 4Å: Chain M: H.133 Chain W: D.136 Ligand excluded by PLIP CD.90: 1 residues within 4Å: Chain M: E.46 Ligand excluded by PLIP CD.91: 3 residues within 4Å: Chain M: E.87, D.95, A.99 Ligand excluded by PLIP CD.92: 5 residues within 4Å: Chain N: D.128 Chain R: D.128 Chain V: D.128 Ligands: CD.120, CD.148 Ligand excluded by PLIP CD.93: 8 residues within 4Å: Chain N: C.127, D.128, E.131 Chain R: E.131 Chain V: E.131 Ligands: CD.94, CD.121, CD.149 Ligand excluded by PLIP CD.94: 5 residues within 4Å: Chain N: H.115, S.119, C.127, E.131 Ligands: CD.93 Ligand excluded by PLIP CD.95: 2 residues within 4Å: Chain N: D.12, R.121 Ligand excluded by PLIP CD.96: 2 residues within 4Å: Chain N: H.133 Chain V: D.136 Ligand excluded by PLIP CD.97: 1 residues within 4Å: Chain N: E.46 Ligand excluded by PLIP CD.98: 3 residues within 4Å: Chain N: E.87, D.95, A.99 Ligand excluded by PLIP CD.99: 5 residues within 4Å: Chain O: D.128 Chain Q: D.128 Chain X: D.128 Ligands: CD.113, CD.162 Ligand excluded by PLIP CD.100: 8 residues within 4Å: Chain O: C.127, D.128, E.131 Chain Q: E.131 Chain X: E.131 Ligands: CD.101, CD.114, CD.163 Ligand excluded by PLIP CD.101: 5 residues within 4Å: Chain O: H.115, S.119, C.127, E.131 Ligands: CD.100 Ligand excluded by PLIP CD.102: 2 residues within 4Å: Chain O: D.12, R.121 Ligand excluded by PLIP CD.103: 2 residues within 4Å: Chain O: H.133 Chain X: D.136 Ligand excluded by PLIP CD.104: 1 residues within 4Å: Chain O: E.46 Ligand excluded by PLIP CD.105: 3 residues within 4Å: Chain O: E.87, D.95, A.99 Ligand excluded by PLIP CD.106: 5 residues within 4Å: Chain P: D.128 Chain S: D.128 Chain U: D.128 Ligands: CD.127, CD.141 Ligand excluded by PLIP CD.107: 8 residues within 4Å: Chain P: C.127, D.128, E.131 Chain S: E.131 Chain U: E.131 Ligands: CD.108, CD.128, CD.142 Ligand excluded by PLIP CD.108: 5 residues within 4Å: Chain P: H.115, S.119, C.127, E.131 Ligands: CD.107 Ligand excluded by PLIP CD.109: 2 residues within 4Å: Chain P: D.12, R.121 Ligand excluded by PLIP CD.110: 2 residues within 4Å: Chain P: H.133 Chain U: D.136 Ligand excluded by PLIP CD.111: 1 residues within 4Å: Chain P: E.46 Ligand excluded by PLIP CD.112: 3 residues within 4Å: Chain P: E.87, D.95, A.99 Ligand excluded by PLIP CD.113: 5 residues within 4Å: Chain O: D.128 Chain Q: D.128 Chain X: D.128 Ligands: CD.99, CD.162 Ligand excluded by PLIP CD.114: 8 residues within 4Å: Chain O: E.131 Chain Q: C.127, D.128, E.131 Chain X: E.131 Ligands: CD.100, CD.115, CD.163 Ligand excluded by PLIP CD.115: 5 residues within 4Å: Chain Q: H.115, S.119, C.127, E.131 Ligands: CD.114 Ligand excluded by PLIP CD.116: 2 residues within 4Å: Chain Q: D.12, R.121 Ligand excluded by PLIP CD.117: 2 residues within 4Å: Chain O: D.136 Chain Q: H.133 Ligand excluded by PLIP CD.118: 1 residues within 4Å: Chain Q: E.46 Ligand excluded by PLIP CD.119: 3 residues within 4Å: Chain Q: E.87, D.95, A.99 Ligand excluded by PLIP CD.120: 5 residues within 4Å: Chain N: D.128 Chain R: D.128 Chain V: D.128 Ligands: CD.92, CD.148 Ligand excluded by PLIP CD.121: 8 residues within 4Å: Chain N: E.131 Chain R: C.127, D.128, E.131 Chain V: E.131 Ligands: CD.93, CD.122, CD.149 Ligand excluded by PLIP CD.122: 5 residues within 4Å: Chain R: H.115, S.119, C.127, E.131 Ligands: CD.121 Ligand excluded by PLIP CD.123: 2 residues within 4Å: Chain R: D.12, R.121 Ligand excluded by PLIP CD.124: 2 residues within 4Å: Chain N: D.136 Chain R: H.133 Ligand excluded by PLIP CD.125: 1 residues within 4Å: Chain R: E.46 Ligand excluded by PLIP CD.126: 3 residues within 4Å: Chain R: E.87, D.95, A.99 Ligand excluded by PLIP CD.127: 5 residues within 4Å: Chain P: D.128 Chain S: D.128 Chain U: D.128 Ligands: CD.106, CD.141 Ligand excluded by PLIP CD.128: 8 residues within 4Å: Chain P: E.131 Chain S: C.127, D.128, E.131 Chain U: E.131 Ligands: CD.107, CD.129, CD.142 Ligand excluded by PLIP CD.129: 5 residues within 4Å: Chain S: H.115, S.119, C.127, E.131 Ligands: CD.128 Ligand excluded by PLIP CD.130: 2 residues within 4Å: Chain S: D.12, R.121 Ligand excluded by PLIP CD.131: 2 residues within 4Å: Chain P: D.136 Chain S: H.133 Ligand excluded by PLIP CD.132: 1 residues within 4Å: Chain S: E.46 Ligand excluded by PLIP CD.133: 3 residues within 4Å: Chain S: E.87, D.95, A.99 Ligand excluded by PLIP CD.134: 5 residues within 4Å: Chain M: D.128 Chain T: D.128 Chain W: D.128 Ligands: CD.85, CD.155 Ligand excluded by PLIP CD.135: 8 residues within 4Å: Chain M: E.131 Chain T: C.127, D.128, E.131 Chain W: E.131 Ligands: CD.86, CD.136, CD.156 Ligand excluded by PLIP CD.136: 5 residues within 4Å: Chain T: H.115, S.119, C.127, E.131 Ligands: CD.135 Ligand excluded by PLIP CD.137: 2 residues within 4Å: Chain T: D.12, R.121 Ligand excluded by PLIP CD.138: 2 residues within 4Å: Chain M: D.136 Chain T: H.133 Ligand excluded by PLIP CD.139: 1 residues within 4Å: Chain T: E.46 Ligand excluded by PLIP CD.140: 3 residues within 4Å: Chain T: E.87, D.95, A.99 Ligand excluded by PLIP CD.141: 5 residues within 4Å: Chain P: D.128 Chain S: D.128 Chain U: D.128 Ligands: CD.106, CD.127 Ligand excluded by PLIP CD.142: 8 residues within 4Å: Chain P: E.131 Chain S: E.131 Chain U: C.127, D.128, E.131 Ligands: CD.107, CD.128, CD.143 Ligand excluded by PLIP CD.143: 5 residues within 4Å: Chain U: H.115, S.119, C.127, E.131 Ligands: CD.142 Ligand excluded by PLIP CD.144: 2 residues within 4Å: Chain U: D.12, R.121 Ligand excluded by PLIP CD.145: 2 residues within 4Å: Chain S: D.136 Chain U: H.133 Ligand excluded by PLIP CD.146: 1 residues within 4Å: Chain U: E.46 Ligand excluded by PLIP CD.147: 3 residues within 4Å: Chain U: E.87, D.95, A.99 Ligand excluded by PLIP CD.148: 5 residues within 4Å: Chain N: D.128 Chain R: D.128 Chain V: D.128 Ligands: CD.92, CD.120 Ligand excluded by PLIP CD.149: 8 residues within 4Å: Chain N: E.131 Chain R: E.131 Chain V: C.127, D.128, E.131 Ligands: CD.93, CD.121, CD.150 Ligand excluded by PLIP CD.150: 5 residues within 4Å: Chain V: H.115, S.119, C.127, E.131 Ligands: CD.149 Ligand excluded by PLIP CD.151: 2 residues within 4Å: Chain V: D.12, R.121 Ligand excluded by PLIP CD.152: 2 residues within 4Å: Chain R: D.136 Chain V: H.133 Ligand excluded by PLIP CD.153: 1 residues within 4Å: Chain V: E.46 Ligand excluded by PLIP CD.154: 3 residues within 4Å: Chain V: E.87, D.95, A.99 Ligand excluded by PLIP CD.155: 5 residues within 4Å: Chain M: D.128 Chain T: D.128 Chain W: D.128 Ligands: CD.85, CD.134 Ligand excluded by PLIP CD.156: 8 residues within 4Å: Chain M: E.131 Chain T: E.131 Chain W: C.127, D.128, E.131 Ligands: CD.86, CD.135, CD.157 Ligand excluded by PLIP CD.157: 5 residues within 4Å: Chain W: H.115, S.119, C.127, E.131 Ligands: CD.156 Ligand excluded by PLIP CD.158: 2 residues within 4Å: Chain W: D.12, R.121 Ligand excluded by PLIP CD.159: 2 residues within 4Å: Chain T: D.136 Chain W: H.133 Ligand excluded by PLIP CD.160: 1 residues within 4Å: Chain W: E.46 Ligand excluded by PLIP CD.161: 3 residues within 4Å: Chain W: E.87, D.95, A.99 Ligand excluded by PLIP CD.162: 5 residues within 4Å: Chain O: D.128 Chain Q: D.128 Chain X: D.128 Ligands: CD.99, CD.113 Ligand excluded by PLIP CD.163: 8 residues within 4Å: Chain O: E.131 Chain Q: E.131 Chain X: C.127, D.128, E.131 Ligands: CD.100, CD.114, CD.164 Ligand excluded by PLIP CD.164: 5 residues within 4Å: Chain X: H.115, S.119, C.127, E.131 Ligands: CD.163 Ligand excluded by PLIP CD.165: 2 residues within 4Å: Chain X: D.12, R.121 Ligand excluded by PLIP CD.166: 2 residues within 4Å: Chain Q: D.136 Chain X: H.133 Ligand excluded by PLIP CD.167: 1 residues within 4Å: Chain X: E.46 Ligand excluded by PLIP CD.168: 3 residues within 4Å: Chain X: E.87, D.95, A.99 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ciambellotti, S. et al., Iron Biomineral Growth from the Initial Nucleation Seed in L-Ferritin. Chemistry (2020)

Release Date

2020-02-19

Peptides

Ferritin light chain: ABCDEFGHIJKLMNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
AAA

C
AAA

D
AAA

E
AAA

F
AAA

G
AAA

H
AAA

I
AAA

J
AAA

K
AAA

L
AAA

M
AAA

N
AAA

O
AAA

P
AAA

Q
AAA

R
AAA

S
AAA

T
AAA

U
AAA

V
AAA

W
AAA

X
AAA

Ferritin light chain

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