SMTL ID : 8x1n.1

Cryo-EM structure of human alpha-fetoprotein

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 3 residues within 4Å: Chain A: N.251, E.254, Q.291 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.22, H.264, H.268, D.280 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.22, A:H.264, A:H.268, A:D.280

4 x PLM: PALMITIC ACID(Non-covalent)

PLM.3: 10 residues within 4Å: Chain A: Y.26, Q.236, A.237, Q.256, L.351, A.352, K.375, Q.378, Y.505, A.506 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.237, A:Q.256, A:L.351, A:A.352 Hydrogen bonds: A:Y.505, A:A.506 PLM.4: 9 residues within 4Å: Chain A: P.176, L.243, K.246, V.262, V.265, G.281, E.282, I.284, M.285 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.176, A:L.243, A:V.262, A:V.265, A:E.282, A:I.284 Salt bridges: A:K.246 PLM.5: 11 residues within 4Å: Chain A: L.411, A.412, S.415, Y.435, A.458, L.469, G.473, E.474, A.477, R.509, S.513 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.411, A:A.412, A:A.458, A:L.469, A:E.474, A:A.477 Hydrogen bonds: A:R.509 PLM.6: 12 residues within 4Å: Chain A: Y.425, N.429, F.526, F.531, K.549, L.553, L.556, I.572, F.575, T.603, R.604, L.607 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.526, A:F.531, A:L.553, A:L.556, A:L.556, A:I.572, A:F.575, A:F.575, A:T.603, A:R.604, A:L.607 Hydrogen bonds: A:N.429 Salt bridges: A:K.549

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, K. et al., Structural characteristics of alpha-fetoprotein, including N-glycosylation, metal ion and fatty acid binding sites. Commun Biol (2024)

Release Date

2024-05-15

Peptides

Alpha-fetoprotein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Alpha-fetoprotein

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