SMTL ID : 3uof.1

Mycobacterium tuberculosis bacterioferritin, BfrA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-24-mer

Ligands

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

FE.1: 6 residues within 4Å: Chain A: Y.27, E.49, E.53, E.96, E.129, H.132 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.53 FE.2: 4 residues within 4Å: Chain A: E.20, E.53, H.56, E.129 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.20, A:E.53, A:E.53, A:H.56, A:E.129 FE.5: 4 residues within 4Å: Chain B: E.20, E.53, H.56, E.129 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.20, B:E.20, B:E.53, B:H.56, B:E.129 FE.6: 6 residues within 4Å: Chain B: Y.27, E.49, E.53, E.96, E.129, H.132 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.49, B:E.53, B:E.96 FE.8: 4 residues within 4Å: Chain C: E.20, E.53, H.56, E.129 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.20, C:E.53, C:E.129 FE.9: 5 residues within 4Å: Chain C: E.49, E.53, E.96, E.129, H.132 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.49, C:E.53 FE.11: 5 residues within 4Å: Chain D: E.20, E.53, H.56, E.129 Ligands: FE.12 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.20, D:E.20, D:E.53, D:E.129 FE.12: 5 residues within 4Å: Chain D: E.53, E.96, E.129, H.132 Ligands: FE.11 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.53, D:E.96, D:E.129 FE.14: 4 residues within 4Å: Chain E: E.49, E.53, E.96, E.129 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:E.53, E:E.53, E:E.129 FE.15: 5 residues within 4Å: Chain E: E.20, E.53, H.56, I.125, E.129 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:E.20, E:E.20, E:H.56, E:E.129 FE.16: 6 residues within 4Å: Chain F: Y.27, E.49, E.53, E.96, E.129, H.132 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.53, F:E.53, F:E.129 FE.17: 4 residues within 4Å: Chain F: E.20, E.53, H.56, E.129 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:E.20, F:E.20, F:E.53, F:H.56, F:E.129 FE.19: 6 residues within 4Å: Chain G: Y.27, E.49, E.53, E.96, E.129, H.132 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:E.53 FE.20: 4 residues within 4Å: Chain G: E.20, E.53, H.56, E.129 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:E.20, G:E.53, G:E.53, G:H.56, G:E.129 FE.23: 4 residues within 4Å: Chain H: E.20, E.53, H.56, E.129 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:E.20, H:E.20, H:E.53, H:H.56, H:E.129 FE.24: 6 residues within 4Å: Chain H: Y.27, E.49, E.53, E.96, E.129, H.132 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:E.49, H:E.53, H:E.96 FE.26: 4 residues within 4Å: Chain I: E.20, E.53, H.56, E.129 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:E.20, I:E.53, I:E.129 FE.27: 5 residues within 4Å: Chain I: E.49, E.53, E.96, E.129, H.132 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:E.49, I:E.53 FE.29: 5 residues within 4Å: Chain J: E.20, E.53, H.56, E.129 Ligands: FE.30 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:E.20, J:E.20, J:E.53, J:E.129 FE.30: 5 residues within 4Å: Chain J: E.53, E.96, E.129, H.132 Ligands: FE.29 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:E.53, J:E.96, J:E.129 FE.32: 4 residues within 4Å: Chain K: E.49, E.53, E.96, E.129 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:E.53, K:E.53, K:E.129 FE.33: 5 residues within 4Å: Chain K: E.20, E.53, H.56, I.125, E.129 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:E.20, K:E.20, K:H.56, K:E.129 FE.34: 6 residues within 4Å: Chain L: Y.27, E.49, E.53, E.96, E.129, H.132 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:E.53, L:E.53, L:E.129 FE.35: 4 residues within 4Å: Chain L: E.20, E.53, H.56, E.129 5 PLIP interactions: 5 interactions with chain L Metal complexes: L:E.20, L:E.20, L:E.53, L:H.56, L:E.129 FE.37: 6 residues within 4Å: Chain M: Y.27, E.49, E.53, E.96, E.129, H.132 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:E.53 FE.38: 4 residues within 4Å: Chain M: E.20, E.53, H.56, E.129 5 PLIP interactions: 5 interactions with chain M Metal complexes: M:E.20, M:E.53, M:E.53, M:H.56, M:E.129 FE.41: 4 residues within 4Å: Chain N: E.20, E.53, H.56, E.129 5 PLIP interactions: 5 interactions with chain N Metal complexes: N:E.20, N:E.20, N:E.53, N:H.56, N:E.129 FE.42: 6 residues within 4Å: Chain N: Y.27, E.49, E.53, E.96, E.129, H.132 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:E.49, N:E.53, N:E.96 FE.44: 4 residues within 4Å: Chain O: E.20, E.53, H.56, E.129 3 PLIP interactions: 3 interactions with chain O Metal complexes: O:E.20, O:E.53, O:E.129 FE.45: 5 residues within 4Å: Chain O: E.49, E.53, E.96, E.129, H.132 2 PLIP interactions: 2 interactions with chain O Metal complexes: O:E.49, O:E.53 FE.47: 5 residues within 4Å: Chain P: E.20, E.53, H.56, E.129 Ligands: FE.48 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:E.20, P:E.20, P:E.53, P:E.129 FE.48: 5 residues within 4Å: Chain P: E.53, E.96, E.129, H.132 Ligands: FE.47 3 PLIP interactions: 3 interactions with chain P Metal complexes: P:E.53, P:E.96, P:E.129 FE.50: 4 residues within 4Å: Chain Q: E.49, E.53, E.96, E.129 3 PLIP interactions: 3 interactions with chain Q Metal complexes: Q:E.53, Q:E.53, Q:E.129 FE.51: 5 residues within 4Å: Chain Q: E.20, E.53, H.56, I.125, E.129 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:E.20, Q:E.20, Q:H.56, Q:E.129 FE.52: 6 residues within 4Å: Chain R: Y.27, E.49, E.53, E.96, E.129, H.132 3 PLIP interactions: 3 interactions with chain R Metal complexes: R:E.53, R:E.53, R:E.129 FE.53: 4 residues within 4Å: Chain R: E.20, E.53, H.56, E.129 5 PLIP interactions: 5 interactions with chain R Metal complexes: R:E.20, R:E.20, R:E.53, R:H.56, R:E.129 FE.55: 6 residues within 4Å: Chain S: Y.27, E.49, E.53, E.96, E.129, H.132 1 PLIP interactions: 1 interactions with chain S Metal complexes: S:E.53 FE.56: 4 residues within 4Å: Chain S: E.20, E.53, H.56, E.129 5 PLIP interactions: 5 interactions with chain S Metal complexes: S:E.20, S:E.53, S:E.53, S:H.56, S:E.129 FE.59: 4 residues within 4Å: Chain T: E.20, E.53, H.56, E.129 5 PLIP interactions: 5 interactions with chain T Metal complexes: T:E.20, T:E.20, T:E.53, T:H.56, T:E.129 FE.60: 6 residues within 4Å: Chain T: Y.27, E.49, E.53, E.96, E.129, H.132 3 PLIP interactions: 3 interactions with chain T Metal complexes: T:E.49, T:E.53, T:E.96 FE.62: 4 residues within 4Å: Chain U: E.20, E.53, H.56, E.129 3 PLIP interactions: 3 interactions with chain U Metal complexes: U:E.20, U:E.53, U:E.129 FE.63: 5 residues within 4Å: Chain U: E.49, E.53, E.96, E.129, H.132 2 PLIP interactions: 2 interactions with chain U Metal complexes: U:E.49, U:E.53 FE.65: 5 residues within 4Å: Chain V: E.20, E.53, H.56, E.129 Ligands: FE.66 4 PLIP interactions: 4 interactions with chain V Metal complexes: V:E.20, V:E.20, V:E.53, V:E.129 FE.66: 5 residues within 4Å: Chain V: E.53, E.96, E.129, H.132 Ligands: FE.65 3 PLIP interactions: 3 interactions with chain V Metal complexes: V:E.53, V:E.96, V:E.129 FE.68: 4 residues within 4Å: Chain W: E.49, E.53, E.96, E.129 3 PLIP interactions: 3 interactions with chain W Metal complexes: W:E.53, W:E.53, W:E.129 FE.69: 5 residues within 4Å: Chain W: E.20, E.53, H.56, I.125, E.129 4 PLIP interactions: 4 interactions with chain W Metal complexes: W:E.20, W:E.20, W:H.56, W:E.129 FE.70: 6 residues within 4Å: Chain X: Y.27, E.49, E.53, E.96, E.129, H.132 3 PLIP interactions: 3 interactions with chain X Metal complexes: X:E.53, X:E.53, X:E.129 FE.71: 4 residues within 4Å: Chain X: E.20, E.53, H.56, E.129 5 PLIP interactions: 5 interactions with chain X Metal complexes: X:E.20, X:E.20, X:E.53, X:H.56, X:E.129

12 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.3: 4 residues within 4Å: Chain A: K.124 Chain T: K.124 Chain V: K.124 Ligands: TRS.61 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain T, 2 interactions with chain V Hydrogen bonds: A:K.124, T:K.124, V:K.124, V:K.124 TRS.7: 6 residues within 4Å: Chain B: V.120, E.123 Chain D: V.120 Chain M: V.120, E.123 Ligands: TRS.39 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:E.123 TRS.18: 5 residues within 4Å: Chain F: V.120, K.124 Chain U: K.124 Chain W: V.120, K.124 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:K.124, F:K.124 TRS.21: 4 residues within 4Å: Chain G: K.124 Chain N: K.124 Chain P: K.124 Ligands: TRS.43 4 PLIP interactions: 1 interactions with chain G, 1 interactions with chain N, 2 interactions with chain P Hydrogen bonds: G:K.124, N:K.124, P:K.124, P:K.124 TRS.25: 6 residues within 4Å: Chain H: V.120, E.123 Chain J: V.120 Chain S: V.120, E.123 Ligands: TRS.57 1 PLIP interactions: 1 interactions with chain S Hydrogen bonds: S:E.123 TRS.36: 5 residues within 4Å: Chain L: V.120, K.124 Chain O: K.124 Chain Q: V.120, K.124 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:K.124, L:K.124 TRS.39: 4 residues within 4Å: Chain B: K.124 Chain D: K.124 Chain M: K.124 Ligands: TRS.7 4 PLIP interactions: 1 interactions with chain M, 1 interactions with chain B, 2 interactions with chain D Hydrogen bonds: M:K.124, B:K.124, D:K.124, D:K.124 TRS.43: 6 residues within 4Å: Chain G: V.120, E.123 Chain N: V.120, E.123 Chain P: V.120 Ligands: TRS.21 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:E.123 TRS.54: 5 residues within 4Å: Chain C: K.124 Chain E: V.120, K.124 Chain R: V.120, K.124 2 PLIP interactions: 2 interactions with chain R Hydrogen bonds: R:K.124, R:K.124 TRS.57: 4 residues within 4Å: Chain H: K.124 Chain J: K.124 Chain S: K.124 Ligands: TRS.25 4 PLIP interactions: 2 interactions with chain J, 1 interactions with chain H, 1 interactions with chain S Hydrogen bonds: J:K.124, J:K.124, H:K.124, S:K.124 TRS.61: 6 residues within 4Å: Chain A: V.120, E.123 Chain T: V.120, E.123 Chain V: V.120 Ligands: TRS.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.123 TRS.72: 5 residues within 4Å: Chain I: K.124 Chain K: V.120, K.124 Chain X: V.120, K.124 2 PLIP interactions: 2 interactions with chain X Hydrogen bonds: X:K.124, X:K.124

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

HEM.4: 14 residues within 4Å: Chain A: L.21, I.24, F.28, R.47, F.51, M.54, E.58 Chain B: L.21, N.25, F.28, F.51, M.54, E.58, Y.73 15 PLIP interactions: 9 interactions with chain A, 6 interactions with chain B, Hydrophobic interactions: A:L.21, A:I.24, A:I.24, A:F.28, A:F.28, A:F.28, A:F.51, A:F.51, A:M.54, B:L.21, B:F.28, B:F.28, B:M.54, B:Y.73 pi-Stacking: B:F.51 HEM.10: 15 residues within 4Å: Chain C: L.21, I.24, N.25, F.28, F.51, M.54, E.58 Chain D: L.21, I.24, N.25, F.28, F.51, M.54, E.58, Y.73 15 PLIP interactions: 7 interactions with chain C, 8 interactions with chain D, Hydrophobic interactions: C:L.21, C:I.24, C:I.24, C:F.28, C:F.28, C:F.51, D:L.21, D:I.24, D:F.28, D:F.28, D:F.51, D:F.51, D:M.54, D:Y.73 pi-Stacking: C:F.51 HEM.13: 16 residues within 4Å: Chain E: L.21, I.24, N.25, F.28, R.47, F.51, M.54, E.58 Chain F: L.21, I.24, F.28, F.51, M.54, A.57, E.58, Y.73 15 PLIP interactions: 7 interactions with chain E, 8 interactions with chain F, Hydrophobic interactions: E:L.21, E:I.24, E:F.28, E:F.51, E:F.51, E:M.54, E:E.58, F:L.21, F:I.24, F:F.28, F:F.28, F:F.51, F:M.54, F:A.57 pi-Stacking: F:F.51 HEM.22: 14 residues within 4Å: Chain G: L.21, I.24, F.28, R.47, F.51, M.54, E.58 Chain H: L.21, N.25, F.28, F.51, M.54, E.58, Y.73 15 PLIP interactions: 6 interactions with chain H, 9 interactions with chain G, Hydrophobic interactions: H:L.21, H:F.28, H:F.28, H:M.54, H:Y.73, G:L.21, G:I.24, G:I.24, G:F.28, G:F.28, G:F.28, G:F.51, G:F.51, G:M.54 pi-Stacking: H:F.51 HEM.28: 15 residues within 4Å: Chain I: L.21, I.24, N.25, F.28, F.51, M.54, E.58 Chain J: L.21, I.24, N.25, F.28, F.51, M.54, E.58, Y.73 15 PLIP interactions: 8 interactions with chain J, 7 interactions with chain I, Hydrophobic interactions: J:L.21, J:I.24, J:F.28, J:F.28, J:F.51, J:F.51, J:M.54, J:Y.73, I:L.21, I:I.24, I:I.24, I:F.28, I:F.28, I:F.51 pi-Stacking: I:F.51 HEM.31: 16 residues within 4Å: Chain K: L.21, I.24, N.25, F.28, R.47, F.51, M.54, E.58 Chain L: L.21, I.24, F.28, F.51, M.54, A.57, E.58, Y.73 15 PLIP interactions: 7 interactions with chain K, 8 interactions with chain L, Hydrophobic interactions: K:L.21, K:I.24, K:F.28, K:F.51, K:F.51, K:M.54, K:E.58, L:L.21, L:I.24, L:F.28, L:F.28, L:F.51, L:M.54, L:A.57 pi-Stacking: L:F.51 HEM.40: 14 residues within 4Å: Chain M: L.21, I.24, F.28, R.47, F.51, M.54, E.58 Chain N: L.21, N.25, F.28, F.51, M.54, E.58, Y.73 15 PLIP interactions: 9 interactions with chain M, 6 interactions with chain N, Hydrophobic interactions: M:L.21, M:I.24, M:I.24, M:F.28, M:F.28, M:F.28, M:F.51, M:F.51, M:M.54, N:L.21, N:F.28, N:F.28, N:M.54, N:Y.73 pi-Stacking: N:F.51 HEM.46: 15 residues within 4Å: Chain O: L.21, I.24, N.25, F.28, F.51, M.54, E.58 Chain P: L.21, I.24, N.25, F.28, F.51, M.54, E.58, Y.73 15 PLIP interactions: 7 interactions with chain O, 8 interactions with chain P, Hydrophobic interactions: O:L.21, O:I.24, O:I.24, O:F.28, O:F.28, O:F.51, P:L.21, P:I.24, P:F.28, P:F.28, P:F.51, P:F.51, P:M.54, P:Y.73 pi-Stacking: O:F.51 HEM.49: 16 residues within 4Å: Chain Q: L.21, I.24, N.25, F.28, R.47, F.51, M.54, E.58 Chain R: L.21, I.24, F.28, F.51, M.54, A.57, E.58, Y.73 15 PLIP interactions: 8 interactions with chain R, 7 interactions with chain Q, Hydrophobic interactions: R:L.21, R:I.24, R:F.28, R:F.28, R:F.51, R:M.54, R:A.57, Q:L.21, Q:I.24, Q:F.28, Q:F.51, Q:F.51, Q:M.54, Q:E.58 pi-Stacking: R:F.51 HEM.58: 14 residues within 4Å: Chain S: L.21, I.24, F.28, R.47, F.51, M.54, E.58 Chain T: L.21, N.25, F.28, F.51, M.54, E.58, Y.73 15 PLIP interactions: 9 interactions with chain S, 6 interactions with chain T, Hydrophobic interactions: S:L.21, S:I.24, S:I.24, S:F.28, S:F.28, S:F.28, S:F.51, S:F.51, S:M.54, T:L.21, T:F.28, T:F.28, T:M.54, T:Y.73 pi-Stacking: T:F.51 HEM.64: 15 residues within 4Å: Chain U: L.21, I.24, N.25, F.28, F.51, M.54, E.58 Chain V: L.21, I.24, N.25, F.28, F.51, M.54, E.58, Y.73 15 PLIP interactions: 8 interactions with chain V, 7 interactions with chain U, Hydrophobic interactions: V:L.21, V:I.24, V:F.28, V:F.28, V:F.51, V:F.51, V:M.54, V:Y.73, U:L.21, U:I.24, U:I.24, U:F.28, U:F.28, U:F.51 pi-Stacking: U:F.51 HEM.67: 16 residues within 4Å: Chain W: L.21, I.24, N.25, F.28, R.47, F.51, M.54, E.58 Chain X: L.21, I.24, F.28, F.51, M.54, A.57, E.58, Y.73 15 PLIP interactions: 8 interactions with chain X, 7 interactions with chain W, Hydrophobic interactions: X:L.21, X:I.24, X:F.28, X:F.28, X:F.51, X:M.54, X:A.57, W:L.21, W:I.24, W:F.28, W:F.51, W:F.51, W:M.54, W:E.58 pi-Stacking: X:F.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2012-11-21

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

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