SMTL ID : 7biz.2 (1 other biounit)

Structure of a B12 binding lipoprotein from Bacteroides thetaiotaomicron

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

monomer

Ligands

1 x CNC: CYANOCOBALAMIN(Non-covalent)

CNC.1: 21 residues within 4Å: Chain A: Q.233, F.234, I.241, H.267, N.299, F.301, G.303, S.304, E.306, L.372, Y.375, H.376, Y.410, W.411, V.435, D.436, W.477, L.478, E.484 Ligands: CA.2, NA.6 25 PLIP interactions: 24 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:F.234, A:F.301, A:F.301, A:Y.375, A:Y.375, A:Y.410, A:D.436, A:W.477, A:L.478, A:E.484 Hydrogen bonds: A:Q.233, A:N.299, A:S.304, A:Y.410, A:Y.410, A:W.411, A:W.411, A:W.477, A:L.478, A:E.484 Water bridges: A:D.302, A:S.304, A:E.306 pi-Stacking: A:F.301 Metal complexes: CNC.1

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: E.306, S.482, E.484 Ligands: CNC.1, NA.6 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.306, A:S.482, A:E.484, A:E.484, H2O.7 CA.3: 6 residues within 4Å: Chain A: D.315, N.317, N.319, L.321, D.323, D.324 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.315, A:L.321, A:D.323, A:D.324

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.4: 7 residues within 4Å: Chain A: Q.404, T.408, G.409, Y.410, W.411, G.476, W.477 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.404, A:W.411, A:W.477 Water bridges: A:Y.410

1 x 15P: POLYETHYLENE GLYCOL (N=34)(Non-functional Binders)

15P.5: 2 residues within 4Å: Chain A: N.222, K.223 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.222, A:N.222

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

NA.6: 7 residues within 4Å: Chain A: N.299, E.306, D.422, S.482, E.484 Ligands: CNC.1, CA.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.299, A:E.306, A:E.484, A:E.484 Water bridges: A:S.304

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Putnam, E.E. et al., Gut Commensal Bacteroidetes Encode a Novel Class of Vitamin B 12 -Binding Proteins. Mbio (2022)

Release Date

2022-03-02

Peptides

Cell surface protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Cell surface protein

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