SMTL ID : 5d8x.1

1.50A resolution structure of BfrB (L68A E81A) from Pseudomonas aeruginosa

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-24-mer

Ligands

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

HEM.1: 19 residues within 4Å: Chain A: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, L.71 Chain B: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, I.59 20 PLIP interactions: 10 interactions with chain A, 10 interactions with chain B, Hydrophobic interactions: A:L.19, A:I.22, A:F.26, A:F.26, A:I.49, A:I.49, A:M.52, A:L.71, B:L.19, B:I.22, B:I.22, B:F.26, B:F.26, B:I.49, B:M.52, B:A.55, B:I.59 Water bridges: A:K.53 Salt bridges: A:K.53, B:K.53 HEM.11: 19 residues within 4Å: Chain C: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, L.71 Chain D: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, I.59 22 PLIP interactions: 11 interactions with chain C, 11 interactions with chain D, Hydrophobic interactions: C:L.19, C:I.22, C:F.26, C:F.26, C:F.26, C:I.49, C:I.49, C:M.52, C:L.71, D:L.19, D:I.22, D:I.22, D:F.26, D:F.26, D:Y.45, D:I.49, D:M.52, D:A.55, D:I.59 Water bridges: C:Y.45 Salt bridges: C:K.53, D:K.53 HEM.17: 19 residues within 4Å: Chain E: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, L.71 Chain F: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, I.59 21 PLIP interactions: 10 interactions with chain E, 11 interactions with chain F, Hydrophobic interactions: E:L.19, E:I.22, E:F.26, E:F.26, E:F.26, E:I.49, E:I.49, E:M.52, E:L.71, F:L.19, F:I.22, F:I.22, F:F.26, F:F.26, F:Y.45, F:I.49, F:M.52, F:A.55, F:I.59 Salt bridges: E:K.53, F:K.53 HEM.25: 19 residues within 4Å: Chain G: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, L.71 Chain H: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, I.59 20 PLIP interactions: 11 interactions with chain G, 9 interactions with chain H, Hydrophobic interactions: G:L.19, G:I.22, G:I.22, G:F.26, G:F.26, G:I.49, G:I.49, G:M.52, G:L.71, H:L.19, H:I.22, H:F.26, H:F.26, H:I.49, H:M.52, H:A.55, H:I.59 Water bridges: G:Y.45 Salt bridges: G:K.53, H:K.53 HEM.34: 19 residues within 4Å: Chain I: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, L.71 Chain J: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, I.59 20 PLIP interactions: 10 interactions with chain I, 10 interactions with chain J, Hydrophobic interactions: I:L.19, I:F.26, I:F.26, I:F.26, I:I.49, I:I.49, I:M.52, I:L.71, J:L.19, J:I.22, J:I.22, J:F.26, J:F.26, J:M.52, J:A.55, J:I.59 Water bridges: I:Y.45, J:K.53 Salt bridges: I:K.53, J:K.53 HEM.39: 19 residues within 4Å: Chain K: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, L.71 Chain L: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, I.59 22 PLIP interactions: 11 interactions with chain K, 11 interactions with chain L, Hydrophobic interactions: K:L.19, K:I.22, K:I.22, K:F.26, K:F.26, K:F.26, K:I.49, K:M.52, K:L.71, L:L.19, L:I.22, L:F.26, L:F.26, L:Y.45, L:I.49, L:I.49, L:M.52, L:A.55, L:I.59 Water bridges: K:Y.45 Salt bridges: K:K.53, L:K.53 HEM.47: 19 residues within 4Å: Chain M: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, L.71 Chain N: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, I.59 20 PLIP interactions: 9 interactions with chain M, 11 interactions with chain N, Hydrophobic interactions: M:L.19, M:I.22, M:F.26, M:F.26, M:I.49, M:M.52, M:L.71, N:L.19, N:I.22, N:I.22, N:F.26, N:F.26, N:I.49, N:I.49, N:M.52, N:A.55, N:I.59 Water bridges: M:K.53 Salt bridges: M:K.53, N:K.53 HEM.55: 19 residues within 4Å: Chain O: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, L.71 Chain P: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, I.59 22 PLIP interactions: 12 interactions with chain O, 10 interactions with chain P, Hydrophobic interactions: O:L.19, O:I.22, O:I.22, O:F.26, O:F.26, O:I.49, O:I.49, O:M.52, O:L.71, P:L.19, P:I.22, P:F.26, P:F.26, P:I.49, P:M.52, P:A.55, P:I.59 Water bridges: O:Y.45, O:K.53, P:K.53 Salt bridges: O:K.53, P:K.53 HEM.57: 19 residues within 4Å: Chain Q: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, L.71 Chain R: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, I.59 23 PLIP interactions: 11 interactions with chain R, 12 interactions with chain Q, Hydrophobic interactions: R:L.19, R:I.22, R:I.22, R:F.26, R:F.26, R:I.49, R:I.49, R:M.52, R:A.55, R:I.59, Q:L.19, Q:I.22, Q:F.26, Q:F.26, Q:I.49, Q:M.52, Q:L.71 Salt bridges: R:K.53, Q:K.53 Water bridges: Q:Y.45, Q:K.53, Q:K.53, Q:K.53 HEM.66: 19 residues within 4Å: Chain S: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, L.71 Chain T: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, I.59 21 PLIP interactions: 11 interactions with chain S, 10 interactions with chain T, Hydrophobic interactions: S:L.19, S:I.22, S:I.22, S:F.26, S:F.26, S:F.26, S:I.49, S:M.52, S:L.71, T:L.19, T:I.22, T:F.26, T:F.26, T:I.49, T:I.49, T:M.52, T:A.55, T:I.59 Water bridges: S:Y.45 Salt bridges: S:K.53, T:K.53 HEM.69: 19 residues within 4Å: Chain U: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, L.71 Chain V: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, I.59 19 PLIP interactions: 10 interactions with chain V, 9 interactions with chain U, Hydrophobic interactions: V:L.19, V:I.22, V:I.22, V:F.26, V:F.26, V:I.49, V:M.52, V:A.55, V:I.59, U:L.19, U:I.22, U:F.26, U:F.26, U:I.49, U:M.52, U:L.71 Salt bridges: V:K.53, U:K.53 Water bridges: U:Y.45 HEM.73: 19 residues within 4Å: Chain W: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, L.71 Chain X: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, I.59 23 PLIP interactions: 13 interactions with chain X, 10 interactions with chain W, Hydrophobic interactions: X:L.19, X:I.22, X:I.22, X:F.26, X:F.26, X:I.49, X:I.49, X:M.52, X:A.55, X:I.59, W:L.19, W:I.22, W:F.26, W:F.26, W:F.26, W:I.49, W:M.52, W:L.71 Water bridges: X:K.53, X:K.53, W:Y.45 Salt bridges: X:K.53, W:K.53

6 x K: POTASSIUM ION(Non-covalent)

K.2: 8 residues within 4Å: Chain A: N.148, Q.151 Chain F: N.148, Q.151 Chain H: N.148, Q.151 Chain Q: N.148, Q.151 No protein-ligand interaction detected (PLIP) K.6: 8 residues within 4Å: Chain B: N.148, Q.151 Chain C: N.148, Q.151 Chain J: N.148, Q.151 Chain W: N.148, Q.151 No protein-ligand interaction detected (PLIP) K.13: 8 residues within 4Å: Chain D: N.148, Q.151 Chain R: N.148, Q.151 Chain T: N.148, Q.151 Chain U: N.148, Q.151 No protein-ligand interaction detected (PLIP) K.18: 8 residues within 4Å: Chain E: N.148, Q.151 Chain I: N.148, Q.151 Chain K: N.148, Q.151 Chain O: N.148, Q.151 No protein-ligand interaction detected (PLIP) K.26: 8 residues within 4Å: Chain G: N.148, Q.151 Chain M: N.148, Q.151 Chain P: N.148, Q.151 Chain V: N.148, Q.151 No protein-ligand interaction detected (PLIP) K.43: 8 residues within 4Å: Chain L: N.148, Q.151 Chain N: N.148, Q.151 Chain S: N.148, Q.151 Chain X: N.148, Q.151 No protein-ligand interaction detected (PLIP)

24 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.3: 6 residues within 4Å: Chain A: M.1, K.2, D.4, V.111, D.113 Chain J: R.102 Ligand excluded by PLIP MRD.7: 6 residues within 4Å: Chain B: M.1, K.2, D.4, V.111, D.113 Chain Q: R.102 Ligand excluded by PLIP MRD.14: 5 residues within 4Å: Chain B: R.102 Chain D: K.2, D.4, V.111, D.113 Ligand excluded by PLIP MRD.19: 6 residues within 4Å: Chain A: R.102 Chain E: M.1, K.2, D.4, V.111, D.113 Ligand excluded by PLIP MRD.20: 6 residues within 4Å: Chain A: E.128, E.129, D.132 Chain E: E.60, R.61, F.64 Ligand excluded by PLIP MRD.23: 7 residues within 4Å: Chain F: M.1, K.2, G.3, D.4, V.111, D.113 Chain O: R.102 Ligand excluded by PLIP MRD.27: 6 residues within 4Å: Chain F: R.102 Chain G: K.2, G.3, D.4, V.111, D.113 Ligand excluded by PLIP MRD.30: 6 residues within 4Å: Chain H: K.2, G.3, D.4, V.111, D.113 Chain V: R.102 Ligand excluded by PLIP MRD.32: 5 residues within 4Å: Chain I: K.2, D.4, V.111, D.113 Chain W: R.102 Ligand excluded by PLIP MRD.37: 5 residues within 4Å: Chain E: E.128, E.129 Chain J: E.60, R.61, F.64 Ligand excluded by PLIP MRD.40: 6 residues within 4Å: Chain K: M.1, K.2, D.4, V.111, D.113 Chain N: R.102 Ligand excluded by PLIP MRD.48: 6 residues within 4Å: Chain M: M.1, K.2, D.4, V.111, D.113 Chain S: R.102 Ligand excluded by PLIP MRD.49: 5 residues within 4Å: Chain M: E.60, R.61, F.64 Chain S: E.128, E.129 Ligand excluded by PLIP MRD.51: 7 residues within 4Å: Chain N: M.1, K.2, G.3, D.4, V.111, D.113 Chain P: R.102 Ligand excluded by PLIP MRD.52: 4 residues within 4Å: Chain N: E.60, R.61, F.64 Chain P: E.129 Ligand excluded by PLIP MRD.54: 5 residues within 4Å: Chain G: R.102 Chain O: K.2, D.4, V.111, D.113 Ligand excluded by PLIP MRD.56: 7 residues within 4Å: Chain K: R.102 Chain P: M.1, K.2, G.3, D.4, V.111, D.113 Ligand excluded by PLIP MRD.61: 6 residues within 4Å: Chain H: E.125, E.129 Chain R: E.60, R.61, F.64, V.115 Ligand excluded by PLIP MRD.64: 5 residues within 4Å: Chain S: E.60, R.61, F.64 Chain U: E.125, E.129 Ligand excluded by PLIP MRD.67: 5 residues within 4Å: Chain T: K.2, D.4, V.111, D.113 Chain X: R.102 Ligand excluded by PLIP MRD.70: 5 residues within 4Å: Chain M: R.102 Chain U: M.1, K.2, V.111, D.113 Ligand excluded by PLIP MRD.71: 5 residues within 4Å: Chain R: R.102 Chain V: K.2, D.4, V.111, D.113 Ligand excluded by PLIP MRD.74: 6 residues within 4Å: Chain L: R.102 Chain W: K.2, G.3, D.4, V.111, D.113 Ligand excluded by PLIP MRD.75: 6 residues within 4Å: Chain C: R.102 Chain X: K.2, G.3, D.4, V.111, D.113 Ligand excluded by PLIP

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

NA.4: 3 residues within 4Å: Chain A: D.34 Chain Q: D.132, T.136 Ligand excluded by PLIP NA.5: 2 residues within 4Å: Chain A: T.136 Chain F: D.34 Ligand excluded by PLIP NA.8: 3 residues within 4Å: Chain B: D.34 Chain J: D.132, T.136 Ligand excluded by PLIP NA.9: 3 residues within 4Å: Chain B: D.132, T.136 Chain C: D.34 Ligand excluded by PLIP NA.12: 3 residues within 4Å: Chain C: D.132, T.136 Chain W: D.34 Ligand excluded by PLIP NA.15: 3 residues within 4Å: Chain D: D.34 Chain T: D.132, T.136 Ligand excluded by PLIP NA.16: 3 residues within 4Å: Chain D: D.132, T.136 Chain R: D.34 Ligand excluded by PLIP NA.21: 3 residues within 4Å: Chain E: D.34 Chain O: D.132, T.136 Ligand excluded by PLIP NA.22: 2 residues within 4Å: Chain E: T.136 Chain I: D.34 Ligand excluded by PLIP NA.24: 3 residues within 4Å: Chain F: D.132, T.136 Chain H: D.34 Ligand excluded by PLIP NA.28: 3 residues within 4Å: Chain G: D.34 Chain V: D.132, T.136 Ligand excluded by PLIP NA.29: 3 residues within 4Å: Chain G: D.132, T.136 Chain P: D.34 Ligand excluded by PLIP NA.31: 3 residues within 4Å: Chain H: D.132, T.136 Chain Q: D.34 Ligand excluded by PLIP NA.35: 3 residues within 4Å: Chain I: D.132, T.136 Chain K: D.34 Ligand excluded by PLIP NA.38: 3 residues within 4Å: Chain J: D.34 Chain W: D.132, T.136 Ligand excluded by PLIP NA.42: 3 residues within 4Å: Chain K: D.132, T.136 Chain O: D.34 Ligand excluded by PLIP NA.45: 3 residues within 4Å: Chain L: D.34 Chain N: D.132, T.136 Ligand excluded by PLIP NA.46: 3 residues within 4Å: Chain L: D.132, T.136 Chain X: D.34 Ligand excluded by PLIP NA.50: 3 residues within 4Å: Chain M: D.34 Chain P: D.132, T.136 Ligand excluded by PLIP NA.53: 3 residues within 4Å: Chain N: D.34 Chain S: D.132, T.136 Ligand excluded by PLIP NA.62: 3 residues within 4Å: Chain R: D.132, T.136 Chain U: D.34 Ligand excluded by PLIP NA.65: 3 residues within 4Å: Chain S: D.34 Chain X: D.132, T.136 Ligand excluded by PLIP NA.68: 3 residues within 4Å: Chain T: D.34 Chain U: D.132, T.136 Ligand excluded by PLIP NA.72: 2 residues within 4Å: Chain M: T.136 Chain V: D.34 Ligand excluded by PLIP

9 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.10: 6 residues within 4Å: Chain C: K.2, G.3, D.4, V.111, D.113 Chain T: R.102 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:D.113 Hydrogen bonds: C:V.111, C:D.113 Water bridges: C:D.4 MPD.33: 6 residues within 4Å: Chain I: E.60, R.61, F.64 Chain W: E.128, E.129, D.132 4 PLIP interactions: 4 interactions with chain I Hydrogen bonds: I:R.61, I:R.61 Water bridges: I:E.60, I:R.61 MPD.36: 7 residues within 4Å: Chain E: R.102 Chain J: M.1, K.2, G.3, D.4, V.111, D.113 4 PLIP interactions: 4 interactions with chain J Hydrophobic interactions: J:D.4, J:D.113 Hydrogen bonds: J:D.4, J:V.111 MPD.41: 5 residues within 4Å: Chain K: E.60, R.61, F.64 Chain N: E.128, E.129 4 PLIP interactions: 1 interactions with chain N, 3 interactions with chain K Hydrophobic interactions: N:E.129, K:F.64 Hydrogen bonds: K:R.61 Water bridges: K:R.61 MPD.44: 6 residues within 4Å: Chain I: R.102 Chain L: K.2, G.3, D.4, V.111, D.113 5 PLIP interactions: 5 interactions with chain L Hydrophobic interactions: L:D.113 Hydrogen bonds: L:D.4, L:V.111, L:D.113 Water bridges: L:D.113 MPD.58: 6 residues within 4Å: Chain D: R.102 Chain Q: K.2, G.3, D.4, V.111, D.113 5 PLIP interactions: 5 interactions with chain Q Hydrophobic interactions: Q:D.113 Hydrogen bonds: Q:D.4, Q:V.111, Q:D.113 Water bridges: Q:D.113 MPD.59: 5 residues within 4Å: Chain D: E.128, E.129 Chain Q: E.60, R.61, F.64 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain Q Hydrophobic interactions: D:E.129, Q:F.64 Hydrogen bonds: Q:R.61, Q:R.61 Water bridges: Q:R.61 MPD.60: 6 residues within 4Å: Chain H: R.102 Chain R: K.2, G.3, D.4, V.111, D.113 4 PLIP interactions: 4 interactions with chain R Hydrophobic interactions: R:D.113 Hydrogen bonds: R:D.4, R:V.111, R:D.113 MPD.63: 6 residues within 4Å: Chain S: K.2, G.3, D.4, V.111, D.113 Chain U: R.102 5 PLIP interactions: 5 interactions with chain S Hydrophobic interactions: S:D.113 Hydrogen bonds: S:D.4, S:V.111 Water bridges: S:D.113, S:D.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y. et al., Characterization of the Bacterioferritin/Bacterioferritin Associated Ferredoxin Protein-Protein Interaction in Solution and Determination of Binding Energy Hot Spots. Biochemistry (2015)

Release Date

2015-09-23

Peptides

Ferroxidase: 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
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Q
Q

R
R

S
S

T
T

U
U

V
V

W
W

X
X

Ferroxidase

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