SMTL ID : 1vlg.1

Crystal structure of Ferritin (TM1128) from Thermotoga maritima at 2.00 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-24-mer

Ligands

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

FE.1: 4 residues within 4Å: Chain A: E.31, E.64, H.67, Q.141 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.31, A:E.64, A:H.67, H2O.2, H2O.3 FE.6: 3 residues within 4Å: Chain B: E.31, E.64, H.67 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.31, B:E.64, B:H.67, H2O.7, H2O.8, H2O.8 FE.12: 3 residues within 4Å: Chain C: E.31, E.64, H.67 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.31, C:E.64, C:H.67, H2O.11, H2O.11 FE.15: 3 residues within 4Å: Chain D: E.31, E.64, H.67 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.31, D:E.64, D:H.67, H2O.13, H2O.14 FE.18: 4 residues within 4Å: Chain E: E.31, E.64, H.67, Q.141 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.31, E:E.64, E:H.67, H2O.18, H2O.19 FE.23: 3 residues within 4Å: Chain F: E.31, E.64, H.67 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.31, F:E.64, F:H.67, H2O.20, H2O.20 FE.27: 3 residues within 4Å: Chain G: E.31, E.64, H.67 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:E.31, G:E.64, G:H.67, H2O.23 FE.29: 3 residues within 4Å: Chain H: E.31, E.64, H.67 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:E.31, H:E.64, H:H.67, H2O.25, H2O.25 FE.32: 4 residues within 4Å: Chain I: E.31, E.64, H.67, Q.141 5 PLIP interactions: 3 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:E.31, I:E.64, I:H.67, H2O.27, H2O.29 FE.37: 3 residues within 4Å: Chain J: E.31, E.64, H.67 6 PLIP interactions: 3 interactions with chain J, 3 Ligand-Water interactions Metal complexes: J:E.31, J:E.64, J:H.67, H2O.32, H2O.33, H2O.33 FE.43: 3 residues within 4Å: Chain K: E.31, E.64, H.67 5 PLIP interactions: 3 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:E.31, K:E.64, K:H.67, H2O.36, H2O.36 FE.46: 3 residues within 4Å: Chain L: E.31, E.64, H.67 5 PLIP interactions: 3 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:E.31, L:E.64, L:H.67, H2O.39, H2O.39 FE.49: 4 residues within 4Å: Chain M: E.31, E.64, H.67, Q.141 5 PLIP interactions: 3 interactions with chain M, 2 Ligand-Water interactions Metal complexes: M:E.31, M:E.64, M:H.67, H2O.43, H2O.44 FE.54: 3 residues within 4Å: Chain N: E.31, E.64, H.67 5 PLIP interactions: 3 interactions with chain N, 2 Ligand-Water interactions Metal complexes: N:E.31, N:E.64, N:H.67, H2O.45, H2O.45 FE.58: 3 residues within 4Å: Chain O: E.31, E.64, H.67 4 PLIP interactions: 3 interactions with chain O, 1 Ligand-Water interactions Metal complexes: O:E.31, O:E.64, O:H.67, H2O.48 FE.60: 3 residues within 4Å: Chain P: E.31, E.64, H.67 5 PLIP interactions: 3 interactions with chain P, 2 Ligand-Water interactions Metal complexes: P:E.31, P:E.64, P:H.67, H2O.50, H2O.50 FE.63: 4 residues within 4Å: Chain Q: E.31, E.64, H.67, Q.141 5 PLIP interactions: 3 interactions with chain Q, 2 Ligand-Water interactions Metal complexes: Q:E.31, Q:E.64, Q:H.67, H2O.52, H2O.54 FE.68: 3 residues within 4Å: Chain R: E.31, E.64, H.67 6 PLIP interactions: 3 interactions with chain R, 3 Ligand-Water interactions Metal complexes: R:E.31, R:E.64, R:H.67, H2O.57, H2O.58, H2O.58 FE.74: 3 residues within 4Å: Chain S: E.31, E.64, H.67 5 PLIP interactions: 3 interactions with chain S, 2 Ligand-Water interactions Metal complexes: S:E.31, S:E.64, S:H.67, H2O.61, H2O.61 FE.77: 3 residues within 4Å: Chain T: E.31, E.64, H.67 5 PLIP interactions: 3 interactions with chain T, 2 Ligand-Water interactions Metal complexes: T:E.31, T:E.64, T:H.67, H2O.64, H2O.64 FE.80: 4 residues within 4Å: Chain U: E.31, E.64, H.67, Q.141 5 PLIP interactions: 3 interactions with chain U, 2 Ligand-Water interactions Metal complexes: U:E.31, U:E.64, U:H.67, H2O.68, H2O.69 FE.85: 3 residues within 4Å: Chain V: E.31, E.64, H.67 5 PLIP interactions: 3 interactions with chain V, 2 Ligand-Water interactions Metal complexes: V:E.31, V:E.64, V:H.67, H2O.70, H2O.70 FE.89: 3 residues within 4Å: Chain W: E.31, E.64, H.67 4 PLIP interactions: 3 interactions with chain W, 1 Ligand-Water interactions Metal complexes: W:E.31, W:E.64, W:H.67, H2O.73 FE.91: 3 residues within 4Å: Chain X: E.31, E.64, H.67 5 PLIP interactions: 3 interactions with chain X, 2 Ligand-Water interactions Metal complexes: X:E.31, X:E.64, X:H.67, H2O.75, H2O.75

42 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 6 residues within 4Å: Chain A: E.109, T.112, Q.113, Y.116, E.145 Chain C: R.78 Ligand excluded by PLIP SO4.3: 7 residues within 4Å: Chain A: Q.161, S.163 Chain B: Q.161, S.163 Chain D: S.163 Chain M: Q.161, S.163 Ligand excluded by PLIP SO4.4: 2 residues within 4Å: Chain A: R.30, F.110 Ligand excluded by PLIP SO4.5: 2 residues within 4Å: Chain A: S.17, E.18 Ligand excluded by PLIP SO4.7: 2 residues within 4Å: Chain B: S.17, E.18 Ligand excluded by PLIP SO4.8: 2 residues within 4Å: Chain B: R.30, F.110 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain B: G.96, I.97, K.98, D.99 Ligand excluded by PLIP SO4.13: 2 residues within 4Å: Chain C: R.30, F.110 Ligand excluded by PLIP SO4.16: 4 residues within 4Å: Chain D: G.96, I.97, K.98, D.99 Ligand excluded by PLIP SO4.17: 5 residues within 4Å: Chain D: E.109, T.112, E.145 Chain E: V.15, R.78 Ligand excluded by PLIP SO4.19: 6 residues within 4Å: Chain E: E.109, T.112, E.145 Chain V: V.15, R.78 Ligands: GOL.88 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain B: E.73 Chain E: H.55, K.58 Ligand excluded by PLIP SO4.24: 5 residues within 4Å: Chain F: N.95, G.96, I.97, K.98, D.99 Ligand excluded by PLIP SO4.30: 6 residues within 4Å: Chain H: E.109, T.112, Y.116, E.145 Chain X: V.15, R.78 Ligand excluded by PLIP SO4.33: 6 residues within 4Å: Chain I: E.109, T.112, Q.113, Y.116, E.145 Chain K: R.78 Ligand excluded by PLIP SO4.34: 7 residues within 4Å: Chain I: Q.161, S.163 Chain J: Q.161, S.163 Chain L: S.163 Chain U: Q.161, S.163 Ligand excluded by PLIP SO4.35: 2 residues within 4Å: Chain I: R.30, F.110 Ligand excluded by PLIP SO4.36: 2 residues within 4Å: Chain I: S.17, E.18 Ligand excluded by PLIP SO4.38: 2 residues within 4Å: Chain J: S.17, E.18 Ligand excluded by PLIP SO4.39: 2 residues within 4Å: Chain J: R.30, F.110 Ligand excluded by PLIP SO4.40: 4 residues within 4Å: Chain J: G.96, I.97, K.98, D.99 Ligand excluded by PLIP SO4.44: 2 residues within 4Å: Chain K: R.30, F.110 Ligand excluded by PLIP SO4.47: 4 residues within 4Å: Chain L: G.96, I.97, K.98, D.99 Ligand excluded by PLIP SO4.48: 5 residues within 4Å: Chain L: E.109, T.112, E.145 Chain M: V.15, R.78 Ligand excluded by PLIP SO4.50: 6 residues within 4Å: Chain F: V.15, R.78 Chain M: E.109, T.112, E.145 Ligands: GOL.26 Ligand excluded by PLIP SO4.51: 3 residues within 4Å: Chain J: E.73 Chain M: H.55, K.58 Ligand excluded by PLIP SO4.55: 5 residues within 4Å: Chain N: N.95, G.96, I.97, K.98, D.99 Ligand excluded by PLIP SO4.61: 6 residues within 4Å: Chain H: V.15, R.78 Chain P: E.109, T.112, Y.116, E.145 Ligand excluded by PLIP SO4.64: 6 residues within 4Å: Chain Q: E.109, T.112, Q.113, Y.116, E.145 Chain S: R.78 Ligand excluded by PLIP SO4.65: 7 residues within 4Å: Chain E: Q.161, S.163 Chain Q: Q.161, S.163 Chain R: Q.161, S.163 Chain T: S.163 Ligand excluded by PLIP SO4.66: 2 residues within 4Å: Chain Q: R.30, F.110 Ligand excluded by PLIP SO4.67: 2 residues within 4Å: Chain Q: S.17, E.18 Ligand excluded by PLIP SO4.69: 2 residues within 4Å: Chain R: S.17, E.18 Ligand excluded by PLIP SO4.70: 2 residues within 4Å: Chain R: R.30, F.110 Ligand excluded by PLIP SO4.71: 4 residues within 4Å: Chain R: G.96, I.97, K.98, D.99 Ligand excluded by PLIP SO4.75: 2 residues within 4Å: Chain S: R.30, F.110 Ligand excluded by PLIP SO4.78: 4 residues within 4Å: Chain T: G.96, I.97, K.98, D.99 Ligand excluded by PLIP SO4.79: 5 residues within 4Å: Chain T: E.109, T.112, E.145 Chain U: V.15, R.78 Ligand excluded by PLIP SO4.81: 6 residues within 4Å: Chain N: V.15, R.78 Chain U: E.109, T.112, E.145 Ligands: GOL.57 Ligand excluded by PLIP SO4.82: 3 residues within 4Å: Chain R: E.73 Chain U: H.55, K.58 Ligand excluded by PLIP SO4.86: 5 residues within 4Å: Chain V: N.95, G.96, I.97, K.98, D.99 Ligand excluded by PLIP SO4.92: 6 residues within 4Å: Chain P: V.15, R.78 Chain X: E.109, T.112, Y.116, E.145 Ligand excluded by PLIP

27 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 3 residues within 4Å: Chain B: H.55, K.58, K.59 Ligand excluded by PLIP GOL.11: 6 residues within 4Å: Chain B: E.109, T.112, Y.116, E.145 Chain J: V.15, R.78 Ligand excluded by PLIP GOL.14: 3 residues within 4Å: Chain C: S.17, E.18, K.19 Ligand excluded by PLIP GOL.21: 2 residues within 4Å: Chain E: R.30, F.110 Ligand excluded by PLIP GOL.22: 6 residues within 4Å: Chain E: K.51, G.52, D.169, R.170, G.173, Q.174 Ligand excluded by PLIP GOL.25: 7 residues within 4Å: Chain F: I.16, S.17, V.20, E.125, K.126, D.127 Ligands: GOL.26 Ligand excluded by PLIP GOL.26: 10 residues within 4Å: Chain F: V.15, I.16, Y.74, R.78, D.127, A.129, T.130 Chain M: Y.116 Ligands: GOL.25, SO4.50 Ligand excluded by PLIP GOL.28: 5 residues within 4Å: Chain G: N.95, G.96, I.97, K.98, D.99 Ligand excluded by PLIP GOL.31: 2 residues within 4Å: Chain H: R.30, F.110 Ligand excluded by PLIP GOL.41: 3 residues within 4Å: Chain J: H.55, K.58, K.59 Ligand excluded by PLIP GOL.42: 6 residues within 4Å: Chain J: E.109, T.112, Y.116, E.145 Chain R: V.15, R.78 Ligand excluded by PLIP GOL.45: 3 residues within 4Å: Chain K: S.17, E.18, K.19 Ligand excluded by PLIP GOL.52: 2 residues within 4Å: Chain M: R.30, F.110 Ligand excluded by PLIP GOL.53: 6 residues within 4Å: Chain M: K.51, G.52, D.169, R.170, G.173, Q.174 Ligand excluded by PLIP GOL.56: 7 residues within 4Å: Chain N: I.16, S.17, V.20, E.125, K.126, D.127 Ligands: GOL.57 Ligand excluded by PLIP GOL.57: 10 residues within 4Å: Chain N: V.15, I.16, Y.74, R.78, D.127, A.129, T.130 Chain U: Y.116 Ligands: GOL.56, SO4.81 Ligand excluded by PLIP GOL.59: 5 residues within 4Å: Chain O: N.95, G.96, I.97, K.98, D.99 Ligand excluded by PLIP GOL.62: 2 residues within 4Å: Chain P: R.30, F.110 Ligand excluded by PLIP GOL.72: 3 residues within 4Å: Chain R: H.55, K.58, K.59 Ligand excluded by PLIP GOL.73: 6 residues within 4Å: Chain B: V.15, R.78 Chain R: E.109, T.112, Y.116, E.145 Ligand excluded by PLIP GOL.76: 3 residues within 4Å: Chain S: S.17, E.18, K.19 Ligand excluded by PLIP GOL.83: 2 residues within 4Å: Chain U: R.30, F.110 Ligand excluded by PLIP GOL.84: 6 residues within 4Å: Chain U: K.51, G.52, D.169, R.170, G.173, Q.174 Ligand excluded by PLIP GOL.87: 7 residues within 4Å: Chain V: I.16, S.17, V.20, E.125, K.126, D.127 Ligands: GOL.88 Ligand excluded by PLIP GOL.88: 10 residues within 4Å: Chain E: Y.116 Chain V: V.15, I.16, Y.74, R.78, D.127, A.129, T.130 Ligands: SO4.19, GOL.87 Ligand excluded by PLIP GOL.90: 5 residues within 4Å: Chain W: N.95, G.96, I.97, K.98, D.99 Ligand excluded by PLIP GOL.93: 2 residues within 4Å: Chain X: R.30, F.110 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of Ferritin (TM1128) from Thermotoga maritima at 2.00 A resolution. To be published

Release Date

2004-08-17

Peptides

ferritin: ABCDEFGHIJKLMNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
A

J
B

K
C

L
D

M
E

N
F

O
G

P
H

Q
A

R
B

S
C

T
D

U
E

V
F

W
G

X
H

ferritin