SMTL ID : 1u7g.1

Crystal Structure of Ammonia Channel AmtB from E. Coli

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-trimer

Ligands

3 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.1: 14 residues within 4Å: Chain A: F.31, F.193, W.245, E.249, L.252, R.253, L.259, S.263, L.296, V.299, T.300, K.303, D.313, V.314 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.31, A:F.193, A:W.245, A:L.259, A:L.259, A:L.259, A:D.313 Hydrogen bonds: A:R.253, A:V.299 Water bridges: A:E.249, A:L.255, A:S.257, A:K.303, A:D.309 BOG.6: 14 residues within 4Å: Chain B: F.31, F.193, W.245, E.249, L.252, R.253, L.259, S.263, L.296, V.299, T.300, K.303, D.313, V.314 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.31, B:F.193, B:W.245, B:L.259, B:L.259, B:L.259, B:D.313 Hydrogen bonds: B:R.253, B:V.299 Water bridges: B:E.249, B:L.255, B:S.257, B:K.303, B:D.309 BOG.11: 14 residues within 4Å: Chain C: F.31, F.193, W.245, E.249, L.252, R.253, L.259, S.263, L.296, V.299, T.300, K.303, D.313, V.314 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:F.31, C:F.193, C:W.245, C:L.259, C:L.259, C:L.259, C:D.313 Hydrogen bonds: C:R.253, C:V.299 Water bridges: C:E.249, C:L.255, C:S.257, C:K.303, C:D.309

3 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.2: 3 residues within 4Å: Chain A: F.107, W.148, S.219 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.161 NH4.7: 3 residues within 4Å: Chain B: F.107, W.148, S.219 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.219 NH4.12: 3 residues within 4Å: Chain C: F.107, W.148, S.219 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:F.161

9 x NH3: AMMONIA(Non-covalent)

NH3.3: 6 residues within 4Å: Chain A: I.28, L.114, L.208, I.266, H.318 Ligands: NH3.5 No protein-ligand interaction detected (PLIP) NH3.4: 5 residues within 4Å: Chain A: M.23, H.168, W.212, F.215 Ligands: NH3.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.168 NH3.5: 6 residues within 4Å: Chain A: L.114, H.168, W.212, H.318 Ligands: NH3.3, NH3.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.318 NH3.8: 6 residues within 4Å: Chain B: I.28, L.114, L.208, I.266, H.318 Ligands: NH3.10 No protein-ligand interaction detected (PLIP) NH3.9: 5 residues within 4Å: Chain B: M.23, H.168, W.212, F.215 Ligands: NH3.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.168 NH3.10: 6 residues within 4Å: Chain B: L.114, H.168, W.212, H.318 Ligands: NH3.8, NH3.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.318 NH3.13: 6 residues within 4Å: Chain C: I.28, L.114, L.208, I.266, H.318 Ligands: NH3.15 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.318 NH3.14: 5 residues within 4Å: Chain C: M.23, H.168, W.212, F.215 Ligands: NH3.15 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.168 NH3.15: 6 residues within 4Å: Chain C: L.114, H.168, W.212, H.318 Ligands: NH3.13, NH3.14 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.318

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Khademi, S. et al., Mechanism of ammonia transport by Amt/MEP/Rh: structure of AmtB at 1.35 A. Science (2004)

Release Date

2004-09-21

Peptides

Probable ammonium transporter: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Membrane

We predict this structure to be a membrane protein.
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Probable ammonium transporter

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