SMTL ID : 8ixu.1

Rat Transcobalamin in Complex with Cobalamin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

1 x B12: COBALAMIN(Non-covalent)

B12.1: 39 residues within 4Å: Chain A: S.101, G.103, S.104, L.107, T.152, S.153, Y.155, Q.156, L.159, H.193, D.197, T.198, N.245, Y.247, S.248, L.251, N.286, M.288, M.289, Q.292, Q.373, S.375, L.376, S.377, G.378, P.379, Y.380, L.381, Y.394, W.395, Q.396, L.397, P.404, L.405, L.406, Q.407, G.408, M.427 Ligands: NO3.2 38 PLIP interactions: 37 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Y.155, A:Y.155, A:Y.155, A:D.197, A:Y.247, A:Y.380, A:Y.380, A:Y.394, A:Y.394, A:L.397, A:L.397 Hydrogen bonds: A:T.152, A:S.153, A:Y.155, A:Q.156, A:D.197, A:D.197, A:N.245, A:S.248, A:Q.292, A:Q.292, A:L.376, A:S.377, A:L.381, A:L.381, A:L.397, A:L.397, A:L.405, A:L.406 Water bridges: A:Y.155, A:Y.155, A:N.286, A:N.286, A:Q.373, A:W.395, A:Q.396, A:Q.396 Metal complexes: B12.1

2 x NO3: NITRATE ION(Non-functional Binders)

NO3.2: 9 residues within 4Å: Chain A: Y.247, A.283, F.284, Q.285, N.286, M.289, Q.407, D.411 Ligands: B12.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:F.284, A:Q.285, A:N.286, A:Q.407 Water bridges: A:N.286, A:D.411, A:K.413 NO3.3: 5 residues within 4Å: Chain A: H.146, G.177, K.178, Y.181, R.221 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.146, A:R.221, A:R.221 Water bridges: A:S.174, A:K.178

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 4 residues within 4Å: Chain A: V.347, S.348, R.361, L.365 Ligand excluded by PLIP CL.5: 6 residues within 4Å: Chain A: T.369, Y.370, S.383, V.384, L.385, G.386 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: P.24, K.25 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: Y.343, R.345, G.366, E.367 Ligand excluded by PLIP

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

NA.8: 3 residues within 4Å: Chain A: R.363, G.366, E.367 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.363, A:G.366

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bokhove, M. et al., The structure of the rat vitamin B 12 transporter TC and its complex with glutathionylcobalamin. J.Biol.Chem. (2024)

Release Date

2024-05-22

Peptides

Transcobalamin-2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Transcobalamin-2

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