SMTL ID : 3kq4.1 (2 other biounits)

Structure of Intrinsic Factor-Cobalamin bound to its receptor Cubilin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

hetero-1-1-mer

Ligands

2 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.1: 7 residues within 4Å: Chain A: Q.297, L.298, Q.363, L.365, N.389, F.390, T.391 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.2: 4 residues within 4Å: Chain B: F.133, P.134, T.160, N.161 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 4 residues within 4Å: Chain B: N.349, N.376, Q.436, L.438 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.436

7 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.4: 5 residues within 4Å: Chain A: N.287, V.311, S.312, V.313, E.325 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.325 Hydrogen bonds: A:V.311, A:V.313 NAG.6: 1 residues within 4Å: Chain B: N.53 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.53 NAG.7: 3 residues within 4Å: Chain B: G.236, N.237, W.263 No protein-ligand interaction detected (PLIP) NAG.8: 1 residues within 4Å: Chain B: N.286 No protein-ligand interaction detected (PLIP) NAG.9: 2 residues within 4Å: Chain B: N.354, T.382 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.382 NAG.10: 2 residues within 4Å: Chain B: N.388, S.429 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.388, B:S.429 NAG.11: 1 residues within 4Å: Chain B: N.401 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.401

1 x B12: COBALAMIN(Non-covalent)

B12.5: 27 residues within 4Å: Chain A: G.66, H.67, L.70, S.106, Y.109, D.147, D.198, Y.200, S.201, L.204, Q.246, T.340, S.341, W.342, G.343, L.344, V.345, V.346, W.362, Q.363, F.364, L.371, N.372, E.373, G.374, D.377, Y.393 22 PLIP interactions: 21 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:L.70, A:D.147, A:W.342, A:W.342, A:V.345, A:N.372, A:Y.393, A:Y.393 Hydrogen bonds: A:D.147, A:Q.246, A:S.341, A:V.346, A:W.362, A:F.364, A:F.364, A:L.371, A:G.374, A:D.377, A:D.377, A:Y.393 Salt bridges: A:H.67 Metal complexes: B12.5

4 x CA: CALCIUM ION(Non-covalent)

CA.12: 5 residues within 4Å: Chain B: E.49, D.57, D.96, D.98, L.99 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.49, B:D.57, B:D.96, B:D.98, B:L.99 CA.13: 6 residues within 4Å: Chain A: K.135 Chain B: E.165, D.174, D.215, I.217, D.218 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.165, B:D.174, B:D.215, B:I.217, B:D.218 CA.14: 7 residues within 4Å: Chain B: E.282, D.290, D.331, E.332, G.333, Q.334, Q.335 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.282, B:D.290, B:D.331, B:D.331, B:G.333 CA.15: 5 residues within 4Å: Chain B: E.397, D.405, T.441, D.442, V.444 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.397, B:D.405, B:D.442, B:V.444

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Andersen, C.B. et al., Structural basis for receptor recognition of vitamin-B(12)-intrinsic factor complexes. Nature (2010)

Release Date

2010-03-09

Peptides

Gastric intrinsic factor: A
Cubilin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Gastric intrinsic factor

Cubilin

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