SMTL ID : 7aae.1

Crystal structure of Human serum albumin in complex with myristic acid at 2.27 Angstrom Resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

monomer

Ligands

6 x MYR: MYRISTIC ACID(Non-covalent)

MYR.1: 12 residues within 4Å: Chain A: R.116, M.122, L.134, Y.137, L.138, I.141, L.153, A.157, Y.160, F.164, L.181, R.185 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.137, A:Y.137, A:Y.137, A:I.141, A:L.153, A:A.157, A:Y.160, A:Y.160, A:Y.160, A:F.164 Salt bridges: A:R.116, A:R.185 MYR.2: 10 residues within 4Å: Chain A: R.9, L.65, F.69, Y.149, P.151, L.250, A.253, R.256, A.257, S.286 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.65, A:F.69, A:P.151, A:L.250, A:A.253 Hydrogen bonds: A:Y.149, A:S.286 Salt bridges: A:R.256 MYR.3: 10 residues within 4Å: Chain A: R.208, K.211, A.212, S.231, T.235, D.323, L.326, G.327, A.349, K.350 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.211, A:A.212, A:L.326 Hydrogen bonds: A:E.353 Salt bridges: A:R.208 MYR.4: 10 residues within 4Å: Chain A: Y.400, N.404, F.506, K.524, A.527, L.528, L.531, V.546, F.550, S.578 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.506, A:F.506, A:A.527, A:L.528, A:L.531, A:L.531, A:V.546, A:F.550, A:F.550 Hydrogen bonds: A:Y.400, A:Y.400 Salt bridges: A:K.524 MYR.5: 12 residues within 4Å: Chain A: L.386, R.409, Y.410, K.413, V.414, V.417, L.422, L.456, L.459, F.487, S.488 Ligands: MYR.6 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.386, A:Y.410, A:Y.410, A:V.417, A:L.422, A:L.456, A:L.459 Hydrogen bonds: A:Y.410, A:Y.410 Salt bridges: A:R.409, A:K.413 MYR.6: 16 residues within 4Å: Chain A: S.341, V.343, R.347, L.386, I.387, N.390, L.406, Y.410, L.429, M.445, A.448, L.452, R.484, P.485 Ligands: MYR.5, PO4.13 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.343, A:L.386, A:I.387, A:N.390, A:L.406, A:A.448 Hydrogen bonds: A:S.341, A:S.341 Salt bridges: A:R.347, A:R.484

5 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.7: 7 residues within 4Å: Chain A: E.16, N.17, L.134, L.138, L.154, A.157, K.158 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.16, A:L.138, A:L.154 MPD.8: 8 residues within 4Å: Chain A: Y.29, H.66, F.69, N.98, L.102, D.248, L.249, L.250 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.29, A:F.69, A:F.69, A:L.102, A:L.249, A:L.250 Hydrogen bonds: A:N.98, A:D.248, A:L.249, A:L.250 Water bridges: A:Y.29 MPD.9: 8 residues within 4Å: Chain A: K.105, Y.147, F.148, Y.149, Q.195, C.244, G.247, C.252 No protein-ligand interaction detected (PLIP) MPD.10: 8 residues within 4Å: Chain A: I.141, H.145, F.148, Y.160, R.185, G.188, K.189, S.192 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.141, A:R.185 Hydrogen bonds: A:Y.160 MPD.11: 7 residues within 4Å: Chain A: L.237, R.256, L.259, I.263, S.286, I.289, A.290 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.237, A:L.259, A:I.263, A:A.290

1 x FMT: FORMIC ACID(Non-functional Binders)

FMT.12: 5 residues within 4Å: Chain A: K.19, A.20, L.23, V.42, K.135 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.135

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.13: 7 residues within 4Å: Chain A: V.343, E.449, L.452, S.453, L.456, R.484 Ligands: MYR.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.449

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maso, L. et al., Unveiling the binding mode of perfluorooctanoic acid to human serum albumin. Protein Sci. (2021)

Release Date

2021-02-24

Peptides

Albumin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

Albumin

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