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

TC:CD320 in complex with nanobody TC-Nb26

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.18 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x CNC: CYANOCOBALAMIN(Non-covalent)

CNC.1: 30 residues within 4Å: Chain A: G.85, Q.86, S.135, Y.137, Q.138, D.176, N.224, Y.226, S.227, N.267, M.270, Q.273, S.357, L.358, S.359, G.360, P.361, Y.362, L.363, F.376, W.377, Q.378, L.379, P.386, L.387, L.388, Q.389, G.390, W.409 Ligands: CA.2 25 PLIP interactions: 24 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Y.137, A:Y.137, A:D.176, A:Y.226, A:Y.362, A:F.376, A:F.376, A:F.376 Hydrogen bonds: A:Q.86, A:Q.138, A:N.224, A:N.224, A:Q.273, A:Q.273, A:L.358, A:S.359, A:S.359, A:S.359, A:L.363, A:L.363, A:L.379, A:L.379, A:L.387, A:L.388 Metal complexes: CNC.1

3 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: Y.226, A.264, Q.266, N.267, Q.389 Ligands: CNC.1 No protein-ligand interaction detected (PLIP) CA.3: 6 residues within 4Å: Chain B: W.99, D.102, H.104, D.106, D.112, E.113 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:W.99, B:D.102, B:H.104, B:D.106, B:D.112, B:E.113 CA.4: 6 residues within 4Å: Chain B: W.21, D.24, D.26, D.28, D.34, E.35 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.24, B:D.26, B:D.28, B:D.34, B:E.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bloch, J.S. et al., Generation of nanobodies targeting the human, transcobalamin-mediated vitamin B 12 uptake route. Faseb J. (2022)

Release Date

2022-03-16

Peptides

Transcobalamin-2: A
CD320 antigen: B
Antitranscobalamin-nanobody TC-Nb26: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

C
E

Transcobalamin-2

CD320 antigen

Antitranscobalamin-nanobody TC-Nb26

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