SMTL ID : 2wtl.1

Crystal structure of BfrA from M. tuberculosis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

homo-24-mer

Ligands

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

FE.1: 5 residues within 4Å: Chain A: E.22, E.55, H.58, I.127, E.131 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.22, A:E.55, A:E.131 FE.2: 5 residues within 4Å: Chain A: Y.29, E.55, E.98, E.131, H.134 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.55, A:E.131, A:H.134, H2O.1, H2O.1 FE.6: 5 residues within 4Å: Chain B: Q.18, E.22, E.55, H.58, E.131 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.22, B:E.22, B:E.55, B:E.131, H2O.2 FE.7: 4 residues within 4Å: Chain B: E.55, E.98, E.131, H.134 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.55, B:E.98, B:E.131 FE.8: 5 residues within 4Å: Chain C: E.22, E.55, H.58, I.127, E.131 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.22, C:E.55, C:H.58, C:E.131 FE.9: 5 residues within 4Å: Chain C: E.51, D.54, E.55, H.58, E.131 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.55, C:E.131, H2O.3 FE.11: 5 residues within 4Å: Chain D: E.22, E.55, H.58, I.127, E.131 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.22, D:E.22, D:E.55, D:E.131 FE.12: 5 residues within 4Å: Chain D: E.51, E.55, E.98, E.131, H.134 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.55, D:E.98, H2O.4 FE.13: 5 residues within 4Å: Chain E: E.22, E.55, H.58, I.127, E.131 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.22, E:E.55, E:E.131, H2O.5, H2O.5 FE.14: 4 residues within 4Å: Chain E: E.55, E.98, E.131, H.134 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:E.55, E:E.98, E:E.131 FE.17: 4 residues within 4Å: Chain F: E.22, E.55, H.58, E.131 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:E.22, F:E.22, F:E.55, F:H.58, F:E.131 FE.18: 4 residues within 4Å: Chain F: E.55, E.98, E.131, H.134 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:E.55, F:E.131 FE.19: 5 residues within 4Å: Chain G: E.22, E.55, H.58, I.127, E.131 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.22, G:E.55, G:E.131 FE.20: 5 residues within 4Å: Chain G: Y.29, E.55, E.98, E.131, H.134 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.55, G:E.131, G:H.134, H2O.7, H2O.8 FE.24: 5 residues within 4Å: Chain H: Q.18, E.22, E.55, H.58, E.131 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:E.22, H:E.22, H:E.55, H:E.131, H2O.8 FE.25: 4 residues within 4Å: Chain H: E.55, E.98, E.131, H.134 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:E.55, H:E.98, H:E.131 FE.26: 5 residues within 4Å: Chain I: E.22, E.55, H.58, I.127, E.131 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:E.22, I:E.55, I:H.58, I:E.131 FE.27: 5 residues within 4Å: Chain I: E.51, D.54, E.55, H.58, E.131 3 PLIP interactions: 2 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:E.55, I:E.131, H2O.10 FE.29: 5 residues within 4Å: Chain J: E.22, E.55, H.58, I.127, E.131 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:E.22, J:E.22, J:E.55, J:E.131 FE.30: 5 residues within 4Å: Chain J: E.51, E.55, E.98, E.131, H.134 3 PLIP interactions: 2 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:E.55, J:E.98, H2O.11 FE.31: 5 residues within 4Å: Chain K: E.22, E.55, H.58, I.127, E.131 5 PLIP interactions: 3 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:E.22, K:E.55, K:E.131, H2O.12, H2O.12 FE.32: 4 residues within 4Å: Chain K: E.55, E.98, E.131, H.134 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:E.55, K:E.98, K:E.131 FE.35: 4 residues within 4Å: Chain L: E.22, E.55, H.58, E.131 5 PLIP interactions: 5 interactions with chain L Metal complexes: L:E.22, L:E.22, L:E.55, L:H.58, L:E.131 FE.36: 4 residues within 4Å: Chain L: E.55, E.98, E.131, H.134 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:E.55, L:E.131 FE.37: 5 residues within 4Å: Chain M: E.22, E.55, H.58, I.127, E.131 3 PLIP interactions: 3 interactions with chain M Metal complexes: M:E.22, M:E.55, M:E.131 FE.38: 5 residues within 4Å: Chain M: Y.29, E.55, E.98, E.131, H.134 5 PLIP interactions: 3 interactions with chain M, 2 Ligand-Water interactions Metal complexes: M:E.55, M:E.131, M:H.134, H2O.14, H2O.14 FE.42: 5 residues within 4Å: Chain N: Q.18, E.22, E.55, H.58, E.131 5 PLIP interactions: 4 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:E.22, N:E.22, N:E.55, N:E.131, H2O.15 FE.43: 4 residues within 4Å: Chain N: E.55, E.98, E.131, H.134 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:E.55, N:E.98, N:E.131 FE.44: 5 residues within 4Å: Chain O: E.22, E.55, H.58, I.127, E.131 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:E.22, O:E.55, O:H.58, O:E.131 FE.45: 5 residues within 4Å: Chain O: E.51, D.54, E.55, H.58, E.131 3 PLIP interactions: 2 interactions with chain O, 1 Ligand-Water interactions Metal complexes: O:E.55, O:E.131, H2O.17 FE.47: 5 residues within 4Å: Chain P: E.22, E.55, H.58, I.127, E.131 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:E.22, P:E.22, P:E.55, P:E.131 FE.48: 5 residues within 4Å: Chain P: E.51, E.55, E.98, E.131, H.134 3 PLIP interactions: 2 interactions with chain P, 1 Ligand-Water interactions Metal complexes: P:E.55, P:E.98, H2O.17 FE.49: 5 residues within 4Å: Chain Q: E.22, E.55, H.58, I.127, E.131 5 PLIP interactions: 3 interactions with chain Q, 2 Ligand-Water interactions Metal complexes: Q:E.22, Q:E.55, Q:E.131, H2O.18, H2O.18 FE.50: 4 residues within 4Å: Chain Q: E.55, E.98, E.131, H.134 3 PLIP interactions: 3 interactions with chain Q Metal complexes: Q:E.55, Q:E.98, Q:E.131 FE.53: 4 residues within 4Å: Chain R: E.22, E.55, H.58, E.131 5 PLIP interactions: 5 interactions with chain R Metal complexes: R:E.22, R:E.22, R:E.55, R:H.58, R:E.131 FE.54: 4 residues within 4Å: Chain R: E.55, E.98, E.131, H.134 2 PLIP interactions: 2 interactions with chain R Metal complexes: R:E.55, R:E.131 FE.55: 5 residues within 4Å: Chain S: E.22, E.55, H.58, I.127, E.131 3 PLIP interactions: 3 interactions with chain S Metal complexes: S:E.22, S:E.55, S:E.131 FE.56: 5 residues within 4Å: Chain S: Y.29, E.55, E.98, E.131, H.134 5 PLIP interactions: 3 interactions with chain S, 2 Ligand-Water interactions Metal complexes: S:E.55, S:E.131, S:H.134, H2O.20, H2O.21 FE.60: 5 residues within 4Å: Chain T: Q.18, E.22, E.55, H.58, E.131 5 PLIP interactions: 4 interactions with chain T, 1 Ligand-Water interactions Metal complexes: T:E.22, T:E.22, T:E.55, T:E.131, H2O.21 FE.61: 4 residues within 4Å: Chain T: E.55, E.98, E.131, H.134 3 PLIP interactions: 3 interactions with chain T Metal complexes: T:E.55, T:E.98, T:E.131 FE.62: 5 residues within 4Å: Chain U: E.22, E.55, H.58, I.127, E.131 4 PLIP interactions: 4 interactions with chain U Metal complexes: U:E.22, U:E.55, U:H.58, U:E.131 FE.63: 5 residues within 4Å: Chain U: E.51, D.54, E.55, H.58, E.131 3 PLIP interactions: 2 interactions with chain U, 1 Ligand-Water interactions Metal complexes: U:E.55, U:E.131, H2O.23 FE.65: 5 residues within 4Å: Chain V: E.22, E.55, H.58, I.127, E.131 4 PLIP interactions: 4 interactions with chain V Metal complexes: V:E.22, V:E.22, V:E.55, V:E.131 FE.66: 5 residues within 4Å: Chain V: E.51, E.55, E.98, E.131, H.134 3 PLIP interactions: 2 interactions with chain V, 1 Ligand-Water interactions Metal complexes: V:E.55, V:E.98, H2O.24 FE.67: 5 residues within 4Å: Chain W: E.22, E.55, H.58, I.127, E.131 5 PLIP interactions: 3 interactions with chain W, 2 Ligand-Water interactions Metal complexes: W:E.22, W:E.55, W:E.131, H2O.25, H2O.25 FE.68: 4 residues within 4Å: Chain W: E.55, E.98, E.131, H.134 3 PLIP interactions: 3 interactions with chain W Metal complexes: W:E.55, W:E.98, W:E.131 FE.71: 4 residues within 4Å: Chain X: E.22, E.55, H.58, E.131 5 PLIP interactions: 5 interactions with chain X Metal complexes: X:E.22, X:E.22, X:E.55, X:H.58, X:E.131 FE.72: 4 residues within 4Å: Chain X: E.55, E.98, E.131, H.134 2 PLIP interactions: 2 interactions with chain X Metal complexes: X:E.55, X:E.131

12 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.3: 7 residues within 4Å: Chain A: Q.156 Chain G: Q.156 Chain M: Q.156 Chain S: Q.156 Ligands: UNX.21, UNX.39, UNX.57 No protein-ligand interaction detected (PLIP) UNX.4: 7 residues within 4Å: Chain A: R.160 Chain G: R.160 Chain M: R.160 Chain S: R.160 Ligands: UNX.22, UNX.40, UNX.58 No protein-ligand interaction detected (PLIP) UNX.15: 11 residues within 4Å: Chain E: Q.156, R.160 Chain K: Q.156, R.160 Chain Q: Q.156, R.160 Chain W: Q.156, R.160 Ligands: UNX.33, UNX.51, UNX.69 No protein-ligand interaction detected (PLIP) UNX.21: 7 residues within 4Å: Chain A: Q.156 Chain G: Q.156 Chain M: Q.156 Chain S: Q.156 Ligands: UNX.3, UNX.39, UNX.57 No protein-ligand interaction detected (PLIP) UNX.22: 7 residues within 4Å: Chain A: R.160 Chain G: R.160 Chain M: R.160 Chain S: R.160 Ligands: UNX.4, UNX.40, UNX.58 No protein-ligand interaction detected (PLIP) UNX.33: 11 residues within 4Å: Chain E: Q.156, R.160 Chain K: Q.156, R.160 Chain Q: Q.156, R.160 Chain W: Q.156, R.160 Ligands: UNX.15, UNX.51, UNX.69 No protein-ligand interaction detected (PLIP) UNX.39: 7 residues within 4Å: Chain A: Q.156 Chain G: Q.156 Chain M: Q.156 Chain S: Q.156 Ligands: UNX.3, UNX.21, UNX.57 No protein-ligand interaction detected (PLIP) UNX.40: 7 residues within 4Å: Chain A: R.160 Chain G: R.160 Chain M: R.160 Chain S: R.160 Ligands: UNX.4, UNX.22, UNX.58 No protein-ligand interaction detected (PLIP) UNX.51: 11 residues within 4Å: Chain E: Q.156, R.160 Chain K: Q.156, R.160 Chain Q: Q.156, R.160 Chain W: Q.156, R.160 Ligands: UNX.15, UNX.33, UNX.69 No protein-ligand interaction detected (PLIP) UNX.57: 7 residues within 4Å: Chain A: Q.156 Chain G: Q.156 Chain M: Q.156 Chain S: Q.156 Ligands: UNX.3, UNX.21, UNX.39 No protein-ligand interaction detected (PLIP) UNX.58: 7 residues within 4Å: Chain A: R.160 Chain G: R.160 Chain M: R.160 Chain S: R.160 Ligands: UNX.4, UNX.22, UNX.40 No protein-ligand interaction detected (PLIP) UNX.69: 11 residues within 4Å: Chain E: Q.156, R.160 Chain K: Q.156, R.160 Chain Q: Q.156, R.160 Chain W: Q.156, R.160 Ligands: UNX.15, UNX.33, UNX.51 No protein-ligand interaction detected (PLIP)

12 x UNL: UNKNOWN LIGAND(Non-covalent)

UNL.5: 19 residues within 4Å: Chain A: I.26, N.27, F.30, R.49, F.53, M.56, A.59, E.60, Y.75 Chain B: L.23, I.26, N.27, F.30, R.49, F.53, M.56, A.59, E.60, Y.75 17 PLIP interactions: 10 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:I.26, A:N.27, A:F.30, A:F.30, A:F.30, A:F.30, A:F.53, A:A.59, A:E.60, A:Y.75, B:I.26, B:F.30, B:F.30, B:A.59, B:E.60, B:Y.75 Hydrogen bonds: B:F.53 UNL.10: 20 residues within 4Å: Chain C: L.23, I.26, N.27, F.30, R.49, F.53, M.56, A.59, E.60, Y.75 Chain D: L.23, I.26, N.27, F.30, R.49, F.53, M.56, R.57, A.59, E.60 16 PLIP interactions: 10 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:L.23, C:I.26, C:I.26, C:F.30, C:F.30, C:F.30, C:A.59, C:E.60, C:Y.75, D:L.23, D:I.26, D:I.26, D:F.30, D:A.59, D:E.60 Hydrogen bonds: C:F.53 UNL.16: 18 residues within 4Å: Chain E: L.23, I.26, N.27, F.30, R.49, F.53, M.56, E.60, Y.75 Chain F: L.23, I.26, N.27, F.30, F.53, M.56, A.59, E.60, Y.75 13 PLIP interactions: 7 interactions with chain E, 6 interactions with chain F Hydrophobic interactions: E:L.23, E:I.26, E:F.30, E:F.30, E:F.30, E:F.53, F:L.23, F:I.26, F:I.26, F:F.30, F:E.60, F:Y.75 Hydrogen bonds: E:Y.75 UNL.23: 19 residues within 4Å: Chain G: I.26, N.27, F.30, R.49, F.53, M.56, A.59, E.60, Y.75 Chain H: L.23, I.26, N.27, F.30, R.49, F.53, M.56, A.59, E.60, Y.75 17 PLIP interactions: 10 interactions with chain G, 7 interactions with chain H Hydrophobic interactions: G:I.26, G:N.27, G:F.30, G:F.30, G:F.30, G:F.30, G:F.53, G:A.59, G:E.60, G:Y.75, H:I.26, H:F.30, H:F.30, H:A.59, H:E.60, H:Y.75 Hydrogen bonds: H:F.53 UNL.28: 20 residues within 4Å: Chain I: L.23, I.26, N.27, F.30, R.49, F.53, M.56, A.59, E.60, Y.75 Chain J: L.23, I.26, N.27, F.30, R.49, F.53, M.56, R.57, A.59, E.60 16 PLIP interactions: 6 interactions with chain J, 10 interactions with chain I Hydrophobic interactions: J:L.23, J:I.26, J:I.26, J:F.30, J:A.59, J:E.60, I:L.23, I:I.26, I:I.26, I:F.30, I:F.30, I:F.30, I:A.59, I:E.60, I:Y.75 Hydrogen bonds: I:F.53 UNL.34: 18 residues within 4Å: Chain K: L.23, I.26, N.27, F.30, R.49, F.53, M.56, E.60, Y.75 Chain L: L.23, I.26, N.27, F.30, F.53, M.56, A.59, E.60, Y.75 13 PLIP interactions: 7 interactions with chain K, 6 interactions with chain L Hydrophobic interactions: K:L.23, K:I.26, K:F.30, K:F.30, K:F.30, K:F.53, L:L.23, L:I.26, L:I.26, L:F.30, L:E.60, L:Y.75 Hydrogen bonds: K:Y.75 UNL.41: 19 residues within 4Å: Chain M: I.26, N.27, F.30, R.49, F.53, M.56, A.59, E.60, Y.75 Chain N: L.23, I.26, N.27, F.30, R.49, F.53, M.56, A.59, E.60, Y.75 17 PLIP interactions: 10 interactions with chain M, 7 interactions with chain N Hydrophobic interactions: M:I.26, M:N.27, M:F.30, M:F.30, M:F.30, M:F.30, M:F.53, M:A.59, M:E.60, M:Y.75, N:I.26, N:F.30, N:F.30, N:A.59, N:E.60, N:Y.75 Hydrogen bonds: N:F.53 UNL.46: 20 residues within 4Å: Chain O: L.23, I.26, N.27, F.30, R.49, F.53, M.56, A.59, E.60, Y.75 Chain P: L.23, I.26, N.27, F.30, R.49, F.53, M.56, R.57, A.59, E.60 16 PLIP interactions: 6 interactions with chain P, 10 interactions with chain O Hydrophobic interactions: P:L.23, P:I.26, P:I.26, P:F.30, P:A.59, P:E.60, O:L.23, O:I.26, O:I.26, O:F.30, O:F.30, O:F.30, O:A.59, O:E.60, O:Y.75 Hydrogen bonds: O:F.53 UNL.52: 18 residues within 4Å: Chain Q: L.23, I.26, N.27, F.30, R.49, F.53, M.56, E.60, Y.75 Chain R: L.23, I.26, N.27, F.30, F.53, M.56, A.59, E.60, Y.75 13 PLIP interactions: 6 interactions with chain R, 7 interactions with chain Q Hydrophobic interactions: R:L.23, R:I.26, R:I.26, R:F.30, R:E.60, R:Y.75, Q:L.23, Q:I.26, Q:F.30, Q:F.30, Q:F.30, Q:F.53 Hydrogen bonds: Q:Y.75 UNL.59: 19 residues within 4Å: Chain S: I.26, N.27, F.30, R.49, F.53, M.56, A.59, E.60, Y.75 Chain T: L.23, I.26, N.27, F.30, R.49, F.53, M.56, A.59, E.60, Y.75 17 PLIP interactions: 10 interactions with chain S, 7 interactions with chain T Hydrophobic interactions: S:I.26, S:N.27, S:F.30, S:F.30, S:F.30, S:F.30, S:F.53, S:A.59, S:E.60, S:Y.75, T:I.26, T:F.30, T:F.30, T:A.59, T:E.60, T:Y.75 Hydrogen bonds: T:F.53 UNL.64: 20 residues within 4Å: Chain U: L.23, I.26, N.27, F.30, R.49, F.53, M.56, A.59, E.60, Y.75 Chain V: L.23, I.26, N.27, F.30, R.49, F.53, M.56, R.57, A.59, E.60 16 PLIP interactions: 10 interactions with chain U, 6 interactions with chain V Hydrophobic interactions: U:L.23, U:I.26, U:I.26, U:F.30, U:F.30, U:F.30, U:A.59, U:E.60, U:Y.75, V:L.23, V:I.26, V:I.26, V:F.30, V:A.59, V:E.60 Hydrogen bonds: U:F.53 UNL.70: 18 residues within 4Å: Chain W: L.23, I.26, N.27, F.30, R.49, F.53, M.56, E.60, Y.75 Chain X: L.23, I.26, N.27, F.30, F.53, M.56, A.59, E.60, Y.75 13 PLIP interactions: 7 interactions with chain W, 6 interactions with chain X Hydrophobic interactions: W:L.23, W:I.26, W:F.30, W:F.30, W:F.30, W:F.53, X:L.23, X:I.26, X:I.26, X:F.30, X:E.60, X:Y.75 Hydrogen bonds: W:Y.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gupta, V. et al., Crystal Structure of Bfra from Mycobacterium Tuberculosis:Incorporation of Selenomethionine Results in Cleavage and Demetallation of Haem. Plos One (2009)

Release Date

2009-12-15

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