SMTL ID : 7qbf.1

TC:CD320 in complex with nanobody TC-Nb34

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

hetero-1-1-1-mer

Ligands

16 x IOD: IODIDE ION(Non-functional Binders)

IOD.1: 4 residues within 4Å: Chain A: K.189, N.192, P.195, R.198 Ligand excluded by PLIP IOD.2: 6 residues within 4Å: Chain A: V.165, H.173, A.178, E.211 Chain C: T.28 Ligands: EDO.28 Ligand excluded by PLIP IOD.3: 8 residues within 4Å: Chain A: H.128, D.159, Y.163, R.200 Chain C: Y.114, Y.116 Ligands: EDO.33, EDO.46 Ligand excluded by PLIP IOD.4: 4 residues within 4Å: Chain A: M.8, D.9, R.253, L.257 Ligand excluded by PLIP IOD.5: 4 residues within 4Å: Chain A: L.387, L.388, Q.389, Y.394 Ligand excluded by PLIP IOD.6: 5 residues within 4Å: Chain A: P.132, S.135, Y.136, R.374, W.409 Ligand excluded by PLIP IOD.7: 3 residues within 4Å: Chain A: F.350, T.351, M.367 Ligand excluded by PLIP IOD.8: 6 residues within 4Å: Chain A: T.351, Y.352, E.353, S.365, M.367, G.368 Ligand excluded by PLIP IOD.9: 5 residues within 4Å: Chain A: H.104, D.107, R.108 Chain B: P.105, P.108 Ligand excluded by PLIP IOD.10: 4 residues within 4Å: Chain A: L.67, H.104, K.105, R.108 Ligand excluded by PLIP IOD.11: 4 residues within 4Å: Chain A: F.376, Q.378, P.386 Ligands: CNC.36 Ligand excluded by PLIP IOD.12: 5 residues within 4Å: Chain A: K.281, D.285, P.289, D.290 Ligands: EDO.19 Ligand excluded by PLIP IOD.39: 4 residues within 4Å: Chain A: L.53, H.56 Chain B: L.15, C.16 Ligand excluded by PLIP IOD.40: 6 residues within 4Å: Chain A: Q.63, Q.64, L.67, K.105 Chain B: W.21 Ligands: EDO.35 Ligand excluded by PLIP IOD.41: 6 residues within 4Å: Chain B: C.10, T.12, S.13, C.29, S.30, D.31 Ligand excluded by PLIP IOD.42: 5 residues within 4Å: Chain A: R.102, G.103 Chain B: D.26, L.27 Ligands: EDO.15 Ligand excluded by PLIP

27 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.13: 7 residues within 4Å: Chain A: R.95, C.98, E.99, F.100, I.287, F.288, P.289 Ligand excluded by PLIP EDO.14: 7 residues within 4Å: Chain A: K.81, Q.86, Q.355, A.356, S.357, Y.362 Ligands: CNC.36 Ligand excluded by PLIP EDO.15: 9 residues within 4Å: Chain A: Q.63, R.102, G.103, K.105, G.106 Chain B: D.26, L.27, D.28 Ligands: IOD.42 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain A: K.121, R.122, G.125, H.126, S.156, K.160 Ligands: EDO.33 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain A: G.223, N.224, L.388 Ligands: EDO.24, EDO.34 Ligand excluded by PLIP EDO.18: 10 residues within 4Å: Chain A: W.23, N.33, I.36, Q.266, N.267, A.268, L.269, L.358, S.359, G.360 Ligand excluded by PLIP EDO.19: 12 residues within 4Å: Chain A: R.41, L.42, R.95, A.96, N.97, K.281, D.285, L.286, P.289, D.290, C.291 Ligands: IOD.12 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain A: L.319, S.320, E.403, R.405, L.406 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain A: S.69, A.70, F.71, D.77, C.78, Q.79 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain A: A.123, G.130, H.131, P.132, H.133, E.373 Ligand excluded by PLIP EDO.23: 3 residues within 4Å: Chain A: W.115, D.119, R.122 Ligand excluded by PLIP EDO.24: 7 residues within 4Å: Chain A: S.174, D.176, N.224, S.227 Ligands: EDO.17, EDO.30, CNC.36 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain A: T.186, K.189, R.190, I.205, S.238 Ligand excluded by PLIP EDO.26: 7 residues within 4Å: Chain A: S.83, M.84, G.85, F.116, T.134, Q.138 Ligands: EDO.32 Ligand excluded by PLIP EDO.27: 2 residues within 4Å: Chain A: L.319, P.324 Ligand excluded by PLIP EDO.28: 8 residues within 4Å: Chain A: H.173, S.174, V.175, A.178, E.211, I.212, A.215 Ligands: IOD.2 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain A: Y.352, E.353, T.354 Ligand excluded by PLIP EDO.30: 7 residues within 4Å: Chain A: H.172, S.174, D.176, T.177, W.409 Ligands: EDO.24, CNC.36 Ligand excluded by PLIP EDO.31: 9 residues within 4Å: Chain A: Q.317, L.380, R.381, D.382, P.383, N.384, T.401, E.403, R.405 Ligand excluded by PLIP EDO.32: 7 residues within 4Å: Chain A: F.116, D.119, E.120, A.123, H.133, T.134 Ligands: EDO.26 Ligand excluded by PLIP EDO.33: 12 residues within 4Å: Chain A: G.125, H.126, D.127, H.128, S.156, D.159, K.160, R.197 Chain C: D.115, Y.116 Ligands: IOD.3, EDO.16 Ligand excluded by PLIP EDO.34: 8 residues within 4Å: Chain A: T.217, E.219, H.221, G.223, N.224, V.225, L.388 Ligands: EDO.17 Ligand excluded by PLIP EDO.35: 10 residues within 4Å: Chain A: Q.64, L.67, G.68, S.69, A.70, F.71, S.72, E.73 Chain B: P.18 Ligands: IOD.40 Ligand excluded by PLIP EDO.43: 4 residues within 4Å: Chain B: G.103, P.105, S.110, E.113 Ligand excluded by PLIP EDO.44: 4 residues within 4Å: Chain C: Q.39, C.45, Y.95, W.117 Ligand excluded by PLIP EDO.45: 1 residues within 4Å: Chain C: R.122 Ligand excluded by PLIP EDO.46: 8 residues within 4Å: Chain A: Y.163, F.168 Chain C: N.97, Y.114, Y.116, W.117, G.118 Ligands: IOD.3 Ligand excluded by PLIP

1 x CNC: CYANOCOBALAMIN(Non-covalent)

CNC.36: 42 residues within 4Å: Chain A: S.83, G.85, Q.86, L.89, T.134, S.135, Y.137, Q.138, L.141, S.174, D.176, T.177, N.224, Y.226, S.227, L.230, N.267, L.269, 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, I.391, W.409 Ligands: IOD.11, EDO.14, EDO.24, EDO.30 40 PLIP interactions: 39 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:L.89, A:Y.137, A:Y.137, A:Y.137, A:L.141, A:D.176, A:Y.226, A:Y.362, A:F.376, A:F.376, A:L.379 Hydrogen bonds: A:Q.86, A:T.134, A:S.135, A:Y.137, A:D.176, A:N.224, A:N.224, A:Y.226, A:S.227, A:Q.273, A:Q.273, A:L.358, A:S.359, A:L.363, A:L.363, A:L.379, A:L.379 Water bridges: A:Y.137, A:Y.137, A:Q.138, A:Q.138, A:Y.226, A:N.267, A:N.267, A:R.374, A:R.374, A:W.377, A:G.390 Metal complexes: CNC.36

2 x CA: CALCIUM ION(Non-covalent)

CA.37: 7 residues within 4Å: Chain A: K.114 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.38: 7 residues within 4Å: Chain A: K.105 Chain B: W.21, D.24, D.26, D.28, D.34, E.35 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:W.21, 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
Anti-transcobalamin-2 nanobody TC-Nb34: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
B

Transcobalamin-2

CD320 antigen

Anti-transcobalamin-2 nanobody TC-Nb34

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