SMTL ID : 2y4d.1

X-ray crystallographic structure of E. coli apo-EfeB

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

13 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain A: G.216, T.217, A.218, R.276, R.327 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.216, A:A.218 Water bridges: A:T.217 Salt bridges: A:R.276, A:R.327 SO4.2: 2 residues within 4Å: Chain A: R.258, K.376 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.376 Salt bridges: A:R.258, A:K.376 SO4.3: 4 residues within 4Å: Chain A: L.152, R.190 Chain B: G.335, V.336 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Water bridges: A:K.189, A:R.190, B:G.335, B:G.335 Salt bridges: A:R.190 Hydrogen bonds: B:V.336 SO4.4: 3 residues within 4Å: Chain A: H.120, S.121, K.139 6 PLIP interactions: 6 interactions with chain A Water bridges: A:H.120, A:S.121, A:S.121, A:S.121 Salt bridges: A:H.120, A:K.139 SO4.5: 2 residues within 4Å: Chain A: R.30, N.31 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.31 Water bridges: A:D.28, A:R.30, A:R.30, A:R.30, A:R.30 Salt bridges: A:R.30 SO4.6: 3 residues within 4Å: Chain A: Q.256, T.337, N.338 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.338 Water bridges: A:Q.256, A:T.337, A:S.339 SO4.14: 6 residues within 4Å: Chain B: K.214, G.216, T.217, A.218, R.276, R.327 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.216, B:T.217, B:T.217, B:A.218 Water bridges: B:K.214, B:R.276, B:R.276, B:R.327 Salt bridges: B:R.276, B:R.327 SO4.15: 3 residues within 4Å: Chain B: R.258, S.339, K.376 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.339, B:S.339 Water bridges: B:K.376 Salt bridges: B:R.258, B:K.376 SO4.16: 4 residues within 4Å: Chain A: G.335, V.336 Chain B: L.152, R.190 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Water bridges: B:R.190, B:R.190, A:G.335 Salt bridges: B:R.190 Hydrogen bonds: A:V.336, A:V.336 SO4.17: 3 residues within 4Å: Chain B: H.120, S.121, K.139 6 PLIP interactions: 6 interactions with chain B Water bridges: B:H.120, B:H.120, B:S.121, B:S.121 Salt bridges: B:H.120, B:K.139 SO4.18: 1 residues within 4Å: Chain B: R.187 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.187, B:R.187, B:R.187 Salt bridges: B:R.187 SO4.19: 2 residues within 4Å: Chain B: T.361, R.365 4 PLIP interactions: 4 interactions with chain B Water bridges: B:T.361, B:R.365, B:R.365 Salt bridges: B:R.365 SO4.20: 4 residues within 4Å: Chain B: R.77, P.88, L.98, H.179 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.77, B:K.178 Salt bridges: B:R.77, B:H.179

3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.7: 6 residues within 4Å: Chain A: A.150, A.151, R.187 Chain B: N.338, S.339, G.340 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.187, A:R.187 PG4.8: 13 residues within 4Å: Chain A: I.255, F.274, H.309, A.313, M.325, R.327, L.346, F.348, F.359, V.362, Q.363, L.366, L.371 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.327 PG4.21: 11 residues within 4Å: Chain B: D.215, I.255, F.274, H.309, A.313, M.325, R.327, L.346, F.348, L.366, L.371 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.215 Water bridges: B:D.215

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.9: 8 residues within 4Å: Chain A: P.47, Q.48, I.194, A.198, A.199, K.202, G.203 Ligands: GOL.10 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.47, A:K.202 Hydrogen bonds: A:Q.48, A:K.202, A:K.202, A:G.203

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 9 residues within 4Å: Chain A: Q.34, T.46, P.47, Q.48, Q.49, N.111, A.199, K.202 Ligands: ACT.9 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.34, A:N.111 Water bridges: A:Q.34, A:Q.34, A:N.164 GOL.11: 5 residues within 4Å: Chain A: A.87, P.88, E.89, G.105 Chain B: Q.279 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Q.279 Water bridges: A:E.89, A:E.89, A:G.104 GOL.12: 3 residues within 4Å: Chain A: H.288, E.289, H.290 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.290, A:H.290 GOL.13: 3 residues within 4Å: Chain A: R.77, L.98, H.179 No protein-ligand interaction detected (PLIP) GOL.22: 1 residues within 4Å: Chain B: E.300 No protein-ligand interaction detected (PLIP) GOL.23: 7 residues within 4Å: Chain B: E.32, Q.34, T.46, P.47, N.111, A.199, K.202 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.34, B:Q.34, B:A.199

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bamford, V.A. et al., Efeb, the Peroxidase Component of the Efeuob Bacterial Fe(II) Transport System, Also Shows Novel Removal of Iron from Heme. To be Published

Release Date

2011-01-26

Peptides

PEROXIDASE YCDB: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PEROXIDASE YCDB

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