SMTL ID : 7qbg.1 (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

1 x CNC: CYANOCOBALAMIN(Non-covalent)

CNC.1: 33 residues within 4Å: Chain A: G.85, Q.86, L.89, T.134, S.135, Y.137, Q.138, L.141, D.176, N.224, Y.226, S.227, L.230, 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 31 PLIP interactions: 30 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:L.89, A:Y.137, A:Y.137, A:L.141, A:Y.226, A:Y.362, A:F.376, A:F.376, A:F.376, A:L.379, A:W.409 Hydrogen bonds: A:Q.86, A:T.134, A:S.135, A:Q.138, A:N.224, A:N.224, A:N.267, A:Q.273, A:Q.273, A:L.358, A:L.363, A:L.363, A:L.379, A:L.379, A:L.387, A:L.388 Water bridges: A:Y.137, A:Y.137, A:Q.389 Metal complexes: CNC.1

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: R.41, L.42, A.96, K.281, D.285, F.288, P.289, D.290, C.291 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.96, A:D.285, A:D.290 GOL.3: 7 residues within 4Å: Chain A: Q.63, R.102, K.105, G.106 Chain B: D.26, L.27, D.28 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.26, B:D.26, B:L.27, A:Q.63, A:Q.63, A:G.106

3 x CA: CALCIUM ION(Non-covalent)

CA.4: 6 residues within 4Å: Chain B: W.99, D.102, H.104, D.106, D.112, E.113 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:W.99, B:D.102, B:H.104, B:D.106, B:D.112 CA.5: 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:W.21, B:D.24, B:D.26, B:D.28, B:D.34 CA.6: 7 residues within 4Å: Chain C: D.33, Q.101, P.102, S.103, N.104, G.105, C.106 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.33, C:D.33, C:Q.101, C:S.103, C:G.105

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
Anti-TC:CD320 nanobody TC-Nb4: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
G

Transcobalamin-2

CD320 antigen

Anti-TC:CD320 nanobody TC-Nb4

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