SMTL ID : 3qb9.1

Mycobacterium tuberculosis bacterioferritin, BfrA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

homo-24-mer

Ligands

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

FE.1: 5 residues within 4Å: Chain A: E.49, E.53, E.96, E.129, H.132 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.53, A:E.96, A:E.129, A:H.132 FE.2: 4 residues within 4Å: Chain A: E.20, E.53, H.56, E.129 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.20, A:E.53, A:H.56, A:E.129, H2O.4 FE.3: 5 residues within 4Å: Chain B: E.20, E.53, H.56, E.129 Ligands: FE.4 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.20, B:E.20, B:H.56, B:E.129, H2O.8 FE.4: 5 residues within 4Å: Chain B: E.53, E.96, E.129, H.132 Ligands: FE.3 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.53, B:E.129, B:E.129 FE.8: 5 residues within 4Å: Chain C: E.20, E.53, H.56, E.129 Ligands: FE.9 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.20, C:E.53, C:H.56, C:E.129, H2O.10 FE.9: 6 residues within 4Å: Chain C: E.49, E.53, E.96, E.129, H.132 Ligands: FE.8 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.53, C:E.96, C:E.129, C:E.129, H2O.10 FE.10: 4 residues within 4Å: Chain D: E.20, E.53, H.56, E.129 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.20, D:E.53, D:E.53, D:H.56, D:E.129 FE.11: 5 residues within 4Å: Chain D: E.49, E.53, E.96, E.129, H.132 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.53, D:E.96, D:E.129 FE.13: 4 residues within 4Å: Chain E: E.20, E.53, H.56, E.129 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.20, E:E.53, E:H.56, E:E.129, H2O.16 FE.14: 5 residues within 4Å: Chain E: E.49, E.53, E.96, E.129, H.132 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:E.53, E:E.96, E:E.129, E:E.129 FE.15: 4 residues within 4Å: Chain F: E.20, E.53, H.56, E.129 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.20, F:E.53, F:E.53, F:H.56, H2O.20 FE.16: 4 residues within 4Å: Chain F: E.53, E.96, E.129, H.132 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.53, F:E.96, F:E.129 FE.17: 5 residues within 4Å: Chain G: E.49, E.53, E.96, E.129, H.132 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:E.53, G:E.96, G:E.129, G:H.132 FE.18: 4 residues within 4Å: Chain G: E.20, E.53, H.56, E.129 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:E.20, G:E.53, G:H.56, G:E.129, H2O.24 FE.19: 5 residues within 4Å: Chain H: E.20, E.53, H.56, E.129 Ligands: FE.20 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:E.20, H:E.20, H:H.56, H:E.129, H2O.27 FE.20: 5 residues within 4Å: Chain H: E.53, E.96, E.129, H.132 Ligands: FE.19 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:E.53, H:E.129, H:E.129 FE.24: 5 residues within 4Å: Chain I: E.20, E.53, H.56, E.129 Ligands: FE.25 5 PLIP interactions: 4 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:E.20, I:E.53, I:H.56, I:E.129, H2O.30 FE.25: 6 residues within 4Å: Chain I: E.49, E.53, E.96, E.129, H.132 Ligands: FE.24 5 PLIP interactions: 4 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:E.53, I:E.96, I:E.129, I:E.129, H2O.30 FE.26: 4 residues within 4Å: Chain J: E.20, E.53, H.56, E.129 5 PLIP interactions: 5 interactions with chain J Metal complexes: J:E.20, J:E.53, J:E.53, J:H.56, J:E.129 FE.27: 5 residues within 4Å: Chain J: E.49, E.53, E.96, E.129, H.132 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:E.53, J:E.96, J:E.129 FE.29: 4 residues within 4Å: Chain K: E.20, E.53, H.56, E.129 5 PLIP interactions: 4 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:E.20, K:E.53, K:H.56, K:E.129, H2O.35 FE.30: 5 residues within 4Å: Chain K: E.49, E.53, E.96, E.129, H.132 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:E.53, K:E.96, K:E.129, K:E.129 FE.31: 4 residues within 4Å: Chain L: E.20, E.53, H.56, E.129 5 PLIP interactions: 4 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:E.20, L:E.53, L:E.53, L:H.56, H2O.40 FE.32: 4 residues within 4Å: Chain L: E.53, E.96, E.129, H.132 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:E.53, L:E.96, L:E.129 FE.33: 5 residues within 4Å: Chain M: E.49, E.53, E.96, E.129, H.132 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:E.53, M:E.96, M:E.129, M:H.132 FE.34: 4 residues within 4Å: Chain M: E.20, E.53, H.56, E.129 5 PLIP interactions: 4 interactions with chain M, 1 Ligand-Water interactions Metal complexes: M:E.20, M:E.53, M:H.56, M:E.129, H2O.43 FE.35: 5 residues within 4Å: Chain N: E.20, E.53, H.56, E.129 Ligands: FE.36 5 PLIP interactions: 4 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:E.20, N:E.20, N:H.56, N:E.129, H2O.47 FE.36: 5 residues within 4Å: Chain N: E.53, E.96, E.129, H.132 Ligands: FE.35 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:E.53, N:E.129, N:E.129 FE.40: 5 residues within 4Å: Chain O: E.20, E.53, H.56, E.129 Ligands: FE.41 5 PLIP interactions: 4 interactions with chain O, 1 Ligand-Water interactions Metal complexes: O:E.20, O:E.53, O:H.56, O:E.129, H2O.50 FE.41: 6 residues within 4Å: Chain O: E.49, E.53, E.96, E.129, H.132 Ligands: FE.40 5 PLIP interactions: 4 interactions with chain O, 1 Ligand-Water interactions Metal complexes: O:E.53, O:E.96, O:E.129, O:E.129, H2O.50 FE.42: 4 residues within 4Å: Chain P: E.20, E.53, H.56, E.129 5 PLIP interactions: 5 interactions with chain P Metal complexes: P:E.20, P:E.53, P:E.53, P:H.56, P:E.129 FE.43: 5 residues within 4Å: Chain P: E.49, E.53, E.96, E.129, H.132 3 PLIP interactions: 3 interactions with chain P Metal complexes: P:E.53, P:E.96, P:E.129 FE.45: 4 residues within 4Å: Chain Q: E.20, E.53, H.56, E.129 5 PLIP interactions: 4 interactions with chain Q, 1 Ligand-Water interactions Metal complexes: Q:E.20, Q:E.53, Q:H.56, Q:E.129, H2O.55 FE.46: 5 residues within 4Å: Chain Q: E.49, E.53, E.96, E.129, H.132 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:E.53, Q:E.96, Q:E.129, Q:E.129 FE.47: 4 residues within 4Å: Chain R: E.20, E.53, H.56, E.129 5 PLIP interactions: 4 interactions with chain R, 1 Ligand-Water interactions Metal complexes: R:E.20, R:E.53, R:E.53, R:H.56, H2O.59 FE.48: 4 residues within 4Å: Chain R: E.53, E.96, E.129, H.132 3 PLIP interactions: 3 interactions with chain R Metal complexes: R:E.53, R:E.96, R:E.129 FE.49: 5 residues within 4Å: Chain S: E.49, E.53, E.96, E.129, H.132 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:E.53, S:E.96, S:E.129, S:H.132 FE.50: 4 residues within 4Å: Chain S: E.20, E.53, H.56, E.129 5 PLIP interactions: 4 interactions with chain S, 1 Ligand-Water interactions Metal complexes: S:E.20, S:E.53, S:H.56, S:E.129, H2O.63 FE.51: 5 residues within 4Å: Chain T: E.20, E.53, H.56, E.129 Ligands: FE.52 5 PLIP interactions: 4 interactions with chain T, 1 Ligand-Water interactions Metal complexes: T:E.20, T:E.20, T:H.56, T:E.129, H2O.66 FE.52: 5 residues within 4Å: Chain T: E.53, E.96, E.129, H.132 Ligands: FE.51 3 PLIP interactions: 3 interactions with chain T Metal complexes: T:E.53, T:E.129, T:E.129 FE.56: 5 residues within 4Å: Chain U: E.20, E.53, H.56, E.129 Ligands: FE.57 5 PLIP interactions: 4 interactions with chain U, 1 Ligand-Water interactions Metal complexes: U:E.20, U:E.53, U:H.56, U:E.129, H2O.69 FE.57: 6 residues within 4Å: Chain U: E.49, E.53, E.96, E.129, H.132 Ligands: FE.56 5 PLIP interactions: 4 interactions with chain U, 1 Ligand-Water interactions Metal complexes: U:E.53, U:E.96, U:E.129, U:E.129, H2O.69 FE.58: 4 residues within 4Å: Chain V: E.20, E.53, H.56, E.129 5 PLIP interactions: 5 interactions with chain V Metal complexes: V:E.20, V:E.53, V:E.53, V:H.56, V:E.129 FE.59: 5 residues within 4Å: Chain V: E.49, E.53, E.96, E.129, H.132 3 PLIP interactions: 3 interactions with chain V Metal complexes: V:E.53, V:E.96, V:E.129 FE.61: 4 residues within 4Å: Chain W: E.20, E.53, H.56, E.129 5 PLIP interactions: 4 interactions with chain W, 1 Ligand-Water interactions Metal complexes: W:E.20, W:E.53, W:H.56, W:E.129, H2O.74 FE.62: 5 residues within 4Å: Chain W: E.49, E.53, E.96, E.129, H.132 4 PLIP interactions: 4 interactions with chain W Metal complexes: W:E.53, W:E.96, W:E.129, W:E.129 FE.63: 4 residues within 4Å: Chain X: E.20, E.53, H.56, E.129 5 PLIP interactions: 4 interactions with chain X, 1 Ligand-Water interactions Metal complexes: X:E.20, X:E.53, X:E.53, X:H.56, H2O.79 FE.64: 4 residues within 4Å: Chain X: E.53, E.96, E.129, H.132 3 PLIP interactions: 3 interactions with chain X Metal complexes: X:E.53, X:E.96, X:E.129

12 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.5: 18 residues within 4Å: Chain A: L.21, I.24, N.25, F.28, R.47, F.51, M.54, R.55, E.58, Y.73 Chain B: L.21, N.25, F.28, F.51, M.54, R.55, E.58, Y.73 18 PLIP interactions: 9 interactions with chain A, 9 interactions with chain B, Hydrophobic interactions: A:L.21, A:I.24, A:F.28, A:F.51, A:F.51, A:M.54, A:Y.73, B:L.21, B:F.28, B:F.28, B:F.51, B:F.51, B:F.51, B:M.54, B:Y.73 Salt bridges: A:R.55, B:R.55 pi-Stacking: A:F.51 HEM.7: 18 residues within 4Å: Chain C: L.21, I.24, N.25, F.28, F.51, M.54, R.55, E.58, Y.73 Chain D: L.21, I.24, N.25, F.28, F.51, M.54, R.55, E.58, Y.73 17 PLIP interactions: 8 interactions with chain C, 9 interactions with chain D, Hydrophobic interactions: C:L.21, C:F.28, C:F.28, C:F.51, C:F.51, C:F.51, C:Y.73, D:L.21, D:I.24, D:F.28, D:F.51, D:F.51, D:F.51, D:M.54, D:Y.73 Salt bridges: C:R.55, D:R.55 HEM.12: 14 residues within 4Å: Chain E: L.21, I.24, F.28, F.51, M.54, R.55, E.58, Y.73 Chain F: N.25, F.28, F.51, M.54, R.55, E.58 17 PLIP interactions: 9 interactions with chain F, 8 interactions with chain E, Hydrophobic interactions: F:F.28, F:F.28, F:F.51, F:F.51, F:F.51, F:M.54, F:E.58, E:L.21, E:I.24, E:F.28, E:M.54, E:E.58, E:Y.73 Hydrogen bonds: F:R.55 Water bridges: F:R.47 Salt bridges: E:R.55 pi-Stacking: E:F.51 HEM.21: 18 residues within 4Å: Chain G: L.21, I.24, N.25, F.28, R.47, F.51, M.54, R.55, E.58, Y.73 Chain H: L.21, N.25, F.28, F.51, M.54, R.55, E.58, Y.73 18 PLIP interactions: 9 interactions with chain H, 9 interactions with chain G, Hydrophobic interactions: H:L.21, H:F.28, H:F.28, H:F.51, H:F.51, H:F.51, H:M.54, H:Y.73, G:L.21, G:I.24, G:F.28, G:F.51, G:F.51, G:M.54, G:Y.73 Salt bridges: H:R.55, G:R.55 pi-Stacking: G:F.51 HEM.23: 18 residues within 4Å: Chain I: L.21, I.24, N.25, F.28, F.51, M.54, R.55, E.58, Y.73 Chain J: L.21, I.24, N.25, F.28, F.51, M.54, R.55, E.58, Y.73 17 PLIP interactions: 8 interactions with chain I, 9 interactions with chain J, Hydrophobic interactions: I:L.21, I:F.28, I:F.28, I:F.51, I:F.51, I:F.51, I:Y.73, J:L.21, J:I.24, J:F.28, J:F.51, J:F.51, J:F.51, J:M.54, J:Y.73 Salt bridges: I:R.55, J:R.55 HEM.28: 14 residues within 4Å: Chain K: L.21, I.24, F.28, F.51, M.54, R.55, E.58, Y.73 Chain L: N.25, F.28, F.51, M.54, R.55, E.58 17 PLIP interactions: 9 interactions with chain L, 8 interactions with chain K, Hydrophobic interactions: L:F.28, L:F.28, L:F.51, L:F.51, L:F.51, L:M.54, L:E.58, K:L.21, K:I.24, K:F.28, K:M.54, K:E.58, K:Y.73 Hydrogen bonds: L:R.55 Water bridges: L:R.47 Salt bridges: K:R.55 pi-Stacking: K:F.51 HEM.37: 18 residues within 4Å: Chain M: L.21, I.24, N.25, F.28, R.47, F.51, M.54, R.55, E.58, Y.73 Chain N: L.21, N.25, F.28, F.51, M.54, R.55, E.58, Y.73 18 PLIP interactions: 9 interactions with chain M, 9 interactions with chain N, Hydrophobic interactions: M:L.21, M:I.24, M:F.28, M:F.51, M:F.51, M:M.54, M:Y.73, N:L.21, N:F.28, N:F.28, N:F.51, N:F.51, N:F.51, N:M.54, N:Y.73 Salt bridges: M:R.55, N:R.55 pi-Stacking: M:F.51 HEM.39: 18 residues within 4Å: Chain O: L.21, I.24, N.25, F.28, F.51, M.54, R.55, E.58, Y.73 Chain P: L.21, I.24, N.25, F.28, F.51, M.54, R.55, E.58, Y.73 17 PLIP interactions: 8 interactions with chain O, 9 interactions with chain P, Hydrophobic interactions: O:L.21, O:F.28, O:F.28, O:F.51, O:F.51, O:F.51, O:Y.73, P:L.21, P:I.24, P:F.28, P:F.51, P:F.51, P:F.51, P:M.54, P:Y.73 Salt bridges: O:R.55, P:R.55 HEM.44: 14 residues within 4Å: Chain Q: L.21, I.24, F.28, F.51, M.54, R.55, E.58, Y.73 Chain R: N.25, F.28, F.51, M.54, R.55, E.58 17 PLIP interactions: 8 interactions with chain Q, 9 interactions with chain R, Hydrophobic interactions: Q:L.21, Q:I.24, Q:F.28, Q:M.54, Q:E.58, Q:Y.73, R:F.28, R:F.28, R:F.51, R:F.51, R:F.51, R:M.54, R:E.58 Salt bridges: Q:R.55 pi-Stacking: Q:F.51 Hydrogen bonds: R:R.55 Water bridges: R:R.47 HEM.53: 18 residues within 4Å: Chain S: L.21, I.24, N.25, F.28, R.47, F.51, M.54, R.55, E.58, Y.73 Chain T: L.21, N.25, F.28, F.51, M.54, R.55, E.58, Y.73 18 PLIP interactions: 9 interactions with chain S, 9 interactions with chain T, Hydrophobic interactions: S:L.21, S:I.24, S:F.28, S:F.51, S:F.51, S:M.54, S:Y.73, T:L.21, T:F.28, T:F.28, T:F.51, T:F.51, T:F.51, T:M.54, T:Y.73 Salt bridges: S:R.55, T:R.55 pi-Stacking: S:F.51 HEM.55: 18 residues within 4Å: Chain U: L.21, I.24, N.25, F.28, F.51, M.54, R.55, E.58, Y.73 Chain V: L.21, I.24, N.25, F.28, F.51, M.54, R.55, E.58, Y.73 17 PLIP interactions: 9 interactions with chain V, 8 interactions with chain U, Hydrophobic interactions: V:L.21, V:I.24, V:F.28, V:F.51, V:F.51, V:F.51, V:M.54, V:Y.73, U:L.21, U:F.28, U:F.28, U:F.51, U:F.51, U:F.51, U:Y.73 Salt bridges: V:R.55, U:R.55 HEM.60: 14 residues within 4Å: Chain W: L.21, I.24, F.28, F.51, M.54, R.55, E.58, Y.73 Chain X: N.25, F.28, F.51, M.54, R.55, E.58 17 PLIP interactions: 8 interactions with chain W, 9 interactions with chain X, Hydrophobic interactions: W:L.21, W:I.24, W:F.28, W:M.54, W:E.58, W:Y.73, X:F.28, X:F.28, X:F.51, X:F.51, X:F.51, X:M.54, X:E.58 Salt bridges: W:R.55 pi-Stacking: W:F.51 Hydrogen bonds: X:R.55 Water bridges: X:R.47

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

NA.6: 2 residues within 4Å: Chain B: Q.154 Chain C: Q.154 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:Q.154, B:Q.154 NA.22: 2 residues within 4Å: Chain H: Q.154 Chain I: Q.154 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain H Hydrogen bonds: I:Q.154, H:Q.154 NA.38: 2 residues within 4Å: Chain N: Q.154 Chain O: Q.154 2 PLIP interactions: 1 interactions with chain N, 1 interactions with chain O Hydrogen bonds: N:Q.154, O:Q.154 NA.54: 2 residues within 4Å: Chain T: Q.154 Chain U: Q.154 2 PLIP interactions: 1 interactions with chain T, 1 interactions with chain U Hydrogen bonds: T:Q.154, U:Q.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McMath, L.M. et al., Mycobacterium tuberculosis bacterioferritin, BfrA. To be Published

Release Date

2012-02-08

Peptides

Bacterioferritin: ABCDEFGHIJKLMNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
A

H
B

I
C

J
D

K
E

L
F

M
A

N
B

O
C

P
D

Q
E

R
F

S
A

T
B

U
C

V
D

W
E

X
F

Bacterioferritin