SMTL ID : 4zrp.1 (1 other biounit)

TC:CD320

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-mer

Ligands

1 x CNC: CYANOCOBALAMIN(Non-covalent)

CNC.1: 31 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.3, GOL.6 39 PLIP interactions: 38 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:D.176, 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 Water bridges: A:H.133, A:S.135, A:Y.137, A:Y.137, A:Y.137, A:Y.137, A:Q.138, A:N.267, A:R.374, A:W.377, A:Q.378, A:G.390, A:W.409 Metal complexes: CNC.1

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 1 residues within 4Å: Chain A: E.375 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.375, H2O.2, H2O.2, H2O.8 CA.3: 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.9: 6 residues within 4Å: Chain B: W.98, D.101, H.103, D.105, D.111, E.112 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:W.98, B:D.101, B:H.103, B:D.105, B:D.111, B:E.112 CA.10: 6 residues within 4Å: Chain B: W.20, D.23, D.25, D.27, D.33, E.34 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.23, B:D.25, B:D.27, B:D.33, B:E.34

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 2 residues within 4Å: Chain A: D.290, L.292 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.290, A:L.292 GOL.5: 6 residues within 4Å: Chain A: R.381, D.382, P.383, N.384, T.401, E.403 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.382, A:N.384, A:E.403, A:E.403, A:R.405 Water bridges: A:Q.317 GOL.6: 4 residues within 4Å: Chain A: S.174, T.177, W.409 Ligands: CNC.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.174, A:S.174, A:T.177 Water bridges: A:H.172, A:T.177 GOL.7: 8 residues within 4Å: Chain A: R.41, L.42, A.96, K.281, D.285, P.289, D.290, C.291 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.41, A:A.96, A:D.285, A:D.290 GOL.8: 7 residues within 4Å: Chain A: Q.63, R.102, G.103, K.105 Chain B: D.25, L.26, D.27 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.63, A:R.102, A:K.105, B:L.26, B:D.27 Water bridges: B:D.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alam, A. et al., Structural basis of transcobalamin recognition by human CD320 receptor. Nat Commun (2016)

Release Date

2016-07-20

Peptides

Transcobalamin-2: A
CD320 antigen: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Transcobalamin-2

CD320 antigen

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