SMTL ID : 3gvy.1

Crystal structure of bacterioferritin from R.sphaeroides

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-24-mer

Ligands

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

HEM.1: 12 residues within 4Å: Chain A: L.19, W.26, R.45, M.52, H.53 Chain C: L.19, V.22, W.26, M.52, H.53, A.55, D.56 12 PLIP interactions: 5 interactions with chain A, 7 interactions with chain C, Hydrophobic interactions: A:L.19, A:W.26, A:W.26, C:L.19, C:V.22, C:W.26, C:W.26, C:M.52, C:A.55 Salt bridges: A:R.45, A:H.53, C:H.53 HEM.3: 16 residues within 4Å: Chain B: L.19, V.22, W.26, R.45, M.52, H.53 Chain T: L.19, V.22, S.23, W.26, R.45, M.52, H.53, A.55, D.56 Ligands: HEM.33 12 PLIP interactions: 5 interactions with chain T, 7 interactions with chain B, Hydrophobic interactions: T:L.19, T:W.26, T:A.55, B:L.19, B:V.22, B:W.26, B:W.26, B:W.26, B:M.52 Salt bridges: T:R.45, B:H.53 pi-Stacking: T:H.53 HEM.6: 12 residues within 4Å: Chain D: L.19, W.26, R.45, M.52, H.53 Chain F: L.19, V.22, W.26, M.52, H.53, A.55, D.56 12 PLIP interactions: 5 interactions with chain D, 7 interactions with chain F, Hydrophobic interactions: D:L.19, D:W.26, D:W.26, F:L.19, F:V.22, F:W.26, F:W.26, F:M.52, F:A.55 Salt bridges: D:R.45, D:H.53, F:H.53 HEM.8: 16 residues within 4Å: Chain E: L.19, V.22, W.26, R.45, M.52, H.53 Chain W: L.19, V.22, S.23, W.26, R.45, M.52, H.53, A.55, D.56 Ligands: HEM.38 12 PLIP interactions: 5 interactions with chain W, 7 interactions with chain E, Hydrophobic interactions: W:L.19, W:W.26, W:A.55, E:L.19, E:V.22, E:W.26, E:W.26, E:W.26, E:M.52 Salt bridges: W:R.45, E:H.53 pi-Stacking: W:H.53 HEM.11: 12 residues within 4Å: Chain G: L.19, W.26, R.45, M.52, H.53 Chain I: L.19, V.22, W.26, M.52, H.53, A.55, D.56 12 PLIP interactions: 7 interactions with chain I, 5 interactions with chain G, Hydrophobic interactions: I:L.19, I:V.22, I:W.26, I:W.26, I:M.52, I:A.55, G:L.19, G:W.26, G:W.26 Salt bridges: I:H.53, G:R.45, G:H.53 HEM.13: 16 residues within 4Å: Chain H: L.19, V.22, W.26, R.45, M.52, H.53 Chain N: L.19, V.22, S.23, W.26, R.45, M.52, H.53, A.55, D.56 Ligands: HEM.23 12 PLIP interactions: 7 interactions with chain H, 5 interactions with chain N, Hydrophobic interactions: H:L.19, H:V.22, H:W.26, H:W.26, H:W.26, H:M.52, N:L.19, N:W.26, N:A.55 Salt bridges: H:H.53, N:R.45 pi-Stacking: N:H.53 HEM.16: 12 residues within 4Å: Chain J: L.19, W.26, R.45, M.52, H.53 Chain L: L.19, V.22, W.26, M.52, H.53, A.55, D.56 12 PLIP interactions: 5 interactions with chain J, 7 interactions with chain L, Hydrophobic interactions: J:L.19, J:W.26, J:W.26, L:L.19, L:V.22, L:W.26, L:W.26, L:M.52, L:A.55 Salt bridges: J:R.45, J:H.53, L:H.53 HEM.18: 16 residues within 4Å: Chain K: L.19, V.22, W.26, R.45, M.52, H.53 Chain Q: L.19, V.22, S.23, W.26, R.45, M.52, H.53, A.55, D.56 Ligands: HEM.28 14 PLIP interactions: 7 interactions with chain K, 7 interactions with chain Q, Hydrophobic interactions: K:L.19, K:V.22, K:W.26, K:W.26, K:W.26, K:M.52, Q:L.19, Q:W.26, Q:M.52, Q:M.52, Q:A.55 Salt bridges: K:H.53, Q:R.45 pi-Stacking: Q:H.53 HEM.21: 12 residues within 4Å: Chain M: L.19, W.26, R.45, M.52, H.53 Chain O: L.19, V.22, W.26, M.52, H.53, A.55, D.56 12 PLIP interactions: 7 interactions with chain O, 5 interactions with chain M, Hydrophobic interactions: O:L.19, O:V.22, O:W.26, O:W.26, O:M.52, O:A.55, M:L.19, M:W.26, M:W.26 Salt bridges: O:H.53, M:R.45, M:H.53 HEM.23: 16 residues within 4Å: Chain H: L.19, V.22, S.23, W.26, R.45, M.52, H.53, A.55, D.56 Chain N: L.19, V.22, W.26, R.45, M.52, H.53 Ligands: HEM.13 12 PLIP interactions: 5 interactions with chain H, 7 interactions with chain N, Hydrophobic interactions: H:L.19, H:W.26, H:A.55, N:L.19, N:V.22, N:W.26, N:W.26, N:W.26, N:M.52 Salt bridges: H:R.45, N:H.53 pi-Stacking: H:H.53 HEM.26: 12 residues within 4Å: Chain P: L.19, W.26, R.45, M.52, H.53 Chain R: L.19, V.22, W.26, M.52, H.53, A.55, D.56 12 PLIP interactions: 7 interactions with chain R, 5 interactions with chain P, Hydrophobic interactions: R:L.19, R:V.22, R:W.26, R:W.26, R:M.52, R:A.55, P:L.19, P:W.26, P:W.26 Salt bridges: R:H.53, P:R.45, P:H.53 HEM.28: 16 residues within 4Å: Chain K: L.19, V.22, S.23, W.26, R.45, M.52, H.53, A.55, D.56 Chain Q: L.19, V.22, W.26, R.45, M.52, H.53 Ligands: HEM.18 14 PLIP interactions: 7 interactions with chain Q, 7 interactions with chain K, Hydrophobic interactions: Q:L.19, Q:V.22, Q:W.26, Q:W.26, Q:W.26, Q:M.52, K:L.19, K:W.26, K:M.52, K:M.52, K:A.55 Salt bridges: Q:H.53, K:R.45 pi-Stacking: K:H.53 HEM.31: 12 residues within 4Å: Chain S: L.19, W.26, R.45, M.52, H.53 Chain U: L.19, V.22, W.26, M.52, H.53, A.55, D.56 12 PLIP interactions: 7 interactions with chain U, 5 interactions with chain S, Hydrophobic interactions: U:L.19, U:V.22, U:W.26, U:W.26, U:M.52, U:A.55, S:L.19, S:W.26, S:W.26 Salt bridges: U:H.53, S:R.45, S:H.53 HEM.33: 16 residues within 4Å: Chain B: L.19, V.22, S.23, W.26, R.45, M.52, H.53, A.55, D.56 Chain T: L.19, V.22, W.26, R.45, M.52, H.53 Ligands: HEM.3 12 PLIP interactions: 5 interactions with chain B, 7 interactions with chain T, Hydrophobic interactions: B:L.19, B:W.26, B:A.55, T:L.19, T:V.22, T:W.26, T:W.26, T:W.26, T:M.52 Salt bridges: B:R.45, T:H.53 pi-Stacking: B:H.53 HEM.36: 12 residues within 4Å: Chain V: L.19, W.26, R.45, M.52, H.53 Chain X: L.19, V.22, W.26, M.52, H.53, A.55, D.56 12 PLIP interactions: 5 interactions with chain V, 7 interactions with chain X, Hydrophobic interactions: V:L.19, V:W.26, V:W.26, X:L.19, X:V.22, X:W.26, X:W.26, X:M.52, X:A.55 Salt bridges: V:R.45, V:H.53, X:H.53 HEM.38: 16 residues within 4Å: Chain E: L.19, V.22, S.23, W.26, R.45, M.52, H.53, A.55, D.56 Chain W: L.19, V.22, W.26, R.45, M.52, H.53 Ligands: HEM.8 12 PLIP interactions: 7 interactions with chain W, 5 interactions with chain E, Hydrophobic interactions: W:L.19, W:V.22, W:W.26, W:W.26, W:W.26, W:M.52, E:L.19, E:W.26, E:A.55 Salt bridges: W:H.53, E:R.45 pi-Stacking: E:H.53

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

FE.2: 5 residues within 4Å: Chain A: E.18, E.51, H.54, E.94, E.127 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.18, A:E.51, A:E.51, A:H.54, A:E.127 FE.4: 4 residues within 4Å: Chain B: E.18, E.51, H.54, E.127 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.18, B:E.51, B:H.54, B:E.127 FE.5: 4 residues within 4Å: Chain C: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.18, C:E.51, C:H.54, C:E.127, C:E.127 FE.7: 5 residues within 4Å: Chain D: E.18, E.51, H.54, E.94, E.127 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.18, D:E.51, D:E.51, D:H.54, D:E.127 FE.9: 4 residues within 4Å: Chain E: E.18, E.51, H.54, E.127 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:E.18, E:E.51, E:H.54, E:E.127 FE.10: 4 residues within 4Å: Chain F: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:E.18, F:E.51, F:H.54, F:E.127, F:E.127 FE.12: 5 residues within 4Å: Chain G: E.18, E.51, H.54, E.94, E.127 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:E.18, G:E.51, G:E.51, G:H.54, G:E.127 FE.14: 4 residues within 4Å: Chain H: E.18, E.51, H.54, E.127 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:E.18, H:E.51, H:H.54, H:E.127 FE.15: 4 residues within 4Å: Chain I: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:E.18, I:E.51, I:H.54, I:E.127, I:E.127 FE.17: 5 residues within 4Å: Chain J: E.18, E.51, H.54, E.94, E.127 5 PLIP interactions: 5 interactions with chain J Metal complexes: J:E.18, J:E.51, J:E.51, J:H.54, J:E.127 FE.19: 4 residues within 4Å: Chain K: E.18, E.51, H.54, E.127 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:E.18, K:E.51, K:H.54, K:E.127 FE.20: 4 residues within 4Å: Chain L: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain L Metal complexes: L:E.18, L:E.51, L:H.54, L:E.127, L:E.127 FE.22: 5 residues within 4Å: Chain M: E.18, E.51, H.54, E.94, E.127 5 PLIP interactions: 5 interactions with chain M Metal complexes: M:E.18, M:E.51, M:E.51, M:H.54, M:E.127 FE.24: 4 residues within 4Å: Chain N: E.18, E.51, H.54, E.127 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:E.18, N:E.51, N:H.54, N:E.127 FE.25: 4 residues within 4Å: Chain O: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain O Metal complexes: O:E.18, O:E.51, O:H.54, O:E.127, O:E.127 FE.27: 5 residues within 4Å: Chain P: E.18, E.51, H.54, E.94, E.127 5 PLIP interactions: 5 interactions with chain P Metal complexes: P:E.18, P:E.51, P:E.51, P:H.54, P:E.127 FE.29: 4 residues within 4Å: Chain Q: E.18, E.51, H.54, E.127 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:E.18, Q:E.51, Q:H.54, Q:E.127 FE.30: 4 residues within 4Å: Chain R: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain R Metal complexes: R:E.18, R:E.51, R:H.54, R:E.127, R:E.127 FE.32: 5 residues within 4Å: Chain S: E.18, E.51, H.54, E.94, E.127 5 PLIP interactions: 5 interactions with chain S Metal complexes: S:E.18, S:E.51, S:E.51, S:H.54, S:E.127 FE.34: 4 residues within 4Å: Chain T: E.18, E.51, H.54, E.127 4 PLIP interactions: 4 interactions with chain T Metal complexes: T:E.18, T:E.51, T:H.54, T:E.127 FE.35: 4 residues within 4Å: Chain U: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain U Metal complexes: U:E.18, U:E.51, U:H.54, U:E.127, U:E.127 FE.37: 5 residues within 4Å: Chain V: E.18, E.51, H.54, E.94, E.127 5 PLIP interactions: 5 interactions with chain V Metal complexes: V:E.18, V:E.51, V:E.51, V:H.54, V:E.127 FE.39: 4 residues within 4Å: Chain W: E.18, E.51, H.54, E.127 4 PLIP interactions: 4 interactions with chain W Metal complexes: W:E.18, W:E.51, W:H.54, W:E.127 FE.40: 4 residues within 4Å: Chain X: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain X Metal complexes: X:E.18, X:E.51, X:H.54, X:E.127, X:E.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nam, K.H. et al., Crystal structure of bacterioferritin from Rhodobacter sphaeroides. Biochem.Biophys.Res.Commun. (2010)

Release Date

2009-12-22

Peptides

Bacterioferritin: ABCDEFGHIJKLMNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

G
A

H
B

I
C

J
A

K
B

L
C

M
A

N
B

O
C

P
A

Q
B

R
C

S
A

T
B

U
C

V
A

W
B

X
C

Bacterioferritin