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

TC:CD320 in complex with nanobody TC-Nb4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.69 Å

Oligo State

hetero-1-1-1-mer

Ligands

3 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: W.21, D.24, D.26, D.28, D.34, E.35 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:W.21, A:D.24, A:D.26, A:D.28, A:D.34 CA.2: 6 residues within 4Å: Chain A: W.99, D.102, H.104, D.106, D.112, E.113 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:W.99, A:H.104, A:D.106, A:D.112, A:E.113 CA.5: 5 residues within 4Å: Chain C: D.33, Q.101, P.102, S.103, G.105 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.33, C:Q.101, C:G.105

1 x CNC: CYANOCOBALAMIN(Non-covalent)

CNC.3: 30 residues within 4Å: Chain B: G.85, Q.86, T.134, 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 25 PLIP interactions: 24 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:Y.137, B:Y.226, B:Y.362, B:F.376, B:F.376, B:W.409 Hydrogen bonds: B:Q.86, B:T.134, B:S.135, B:Q.138, B:N.224, B:N.224, B:Y.226, B:Q.273, B:Q.273, B:L.358, B:S.359, B:L.363, B:L.363, B:L.379, B:L.387 Water bridges: B:Y.137, B:Y.137, B:Q.389 Metal complexes: CNC.3

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: D.26, L.27, D.28 Chain B: K.59, Q.63, R.102, G.103 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.63, B:R.102, A:D.28

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

CD320 antigen: A
Transcobalamin-2: B
Anti-TC:CD320 nanobody TC-Nb4: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
E

CD320 antigen

Transcobalamin-2

Anti-TC:CD320 nanobody TC-Nb4

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