SMTL ID : 7wgu.1

Crystal structure of metal-binding protein EfeO from Escherichia coli

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

30 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 3 residues within 4Å: Chain A: G.60, F.61, S.62 Ligand excluded by PLIP EDO.2: 5 residues within 4Å: Chain A: Q.29, R.54, K.64, M.65, T.66 Ligand excluded by PLIP EDO.3: 5 residues within 4Å: Chain A: E.93 Chain B: A.25, P.71, G.92, E.93 Ligand excluded by PLIP EDO.4: 3 residues within 4Å: Chain A: K.143, A.146, L.147 Ligand excluded by PLIP EDO.5: 8 residues within 4Å: Chain A: K.145, A.146, Y.148, A.149, P.150, F.199, T.261, W.264 Ligand excluded by PLIP EDO.6: 8 residues within 4Å: Chain A: E.159, P.160, E.163, G.237, G.238, G.241, L.242, E.245 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: T.189, Q.209, Y.210, Q.213 Ligand excluded by PLIP EDO.8: 2 residues within 4Å: Chain A: Q.63, K.64 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: F.199, G.200, D.201, N.202 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: Q.153, W.264, Q.267, E.271, R.310, F.315 Ligand excluded by PLIP EDO.11: 2 residues within 4Å: Chain A: G.345, V.346 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: Y.117, E.121, R.157, E.271 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: P.18, M.19, T.20 Ligand excluded by PLIP EDO.14: 2 residues within 4Å: Chain A: T.216, D.220 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: T.123, V.126, T.127, Q.222 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain A: I.21, T.22 Chain B: V.4, Q.6 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain B: G.72, I.89, V.90, K.91 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain B: A.103, S.106, Q.283, K.286 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain B: E.159, E.163, G.238, G.241, L.242 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain B: T.204, G.206, M.207, D.208 Ligand excluded by PLIP EDO.25: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain B: M.19, T.20, K.85, G.86, K.87 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain A: V.48, K.85 Chain B: K.115, S.226, E.227, L.228 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain B: Q.29, R.54, K.64, M.65, T.66 Ligand excluded by PLIP EDO.29: 6 residues within 4Å: Chain A: E.227, L.228, A.229 Chain B: E.41, E.43, L.81 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Chain A: G.47, V.48 Chain B: T.112 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain B: E.244, A.247, A.248, K.330, T.334 Ligand excluded by PLIP EDO.32: 3 residues within 4Å: Chain B: A.293, D.296, A.297 Ligand excluded by PLIP EDO.33: 1 residues within 4Å: Chain A: T.112 Ligand excluded by PLIP EDO.34: 3 residues within 4Å: Chain B: P.18, M.19, T.20 Ligand excluded by PLIP

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

ACT.16: 1 residues within 4Å: Chain A: G.206 No protein-ligand interaction detected (PLIP)

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.17: 11 residues within 4Å: Chain A: P.5, Q.6, V.7, V.23, N.24, T.28 Chain B: P.5, V.7, V.23, N.24, T.28 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.6, A:N.24, A:N.24, A:T.28, B:N.24, B:N.24

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

SO4.18: 5 residues within 4Å: Chain A: F.165, S.166, D.167, L.168, R.224 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.166, A:D.167, A:L.168 Water bridges: A:S.166, A:R.224, A:R.224 Salt bridges: A:R.224

1 x ZN: ZINC ION(Non-covalent)

ZN.19: 5 residues within 4Å: Chain B: E.156, E.159, D.173, K.250, E.255 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.156, B:E.159, B:D.173, H2O.8, H2O.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakatsuji, S. et al., Crystal structures of EfeB and EfeO in a bacterial siderophore-independent iron transport system. Biochem.Biophys.Res.Commun. (2022)

Release Date

2022-12-14

Peptides

Iron uptake system protein EfeO: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Iron uptake system protein EfeO