SMTL ID : 6fak.1

Human afamin orthorhombic crystal form by controlled hydration

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

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.1: 6 residues within 4Å: Chain A: Y.106, L.207, K.208, F.209, G.210, N.467 No protein-ligand interaction detected (PLIP)

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

NAG.2: 1 residues within 4Å: Chain A: N.88 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.88 NAG.3: 3 residues within 4Å: Chain A: N.381, T.384, E.385 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.384 Hydrogen bonds: A:N.381, A:E.385

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 5 residues within 4Å: Chain A: N.149, P.150, F.151, V.152, S.196 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.5: 2 residues within 4Å: Chain A: G.113, L.115 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.113

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 2 residues within 4Å: Chain A: Y.191, A.194 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.194 Water bridges: A:Y.191

2 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.7: 7 residues within 4Å: Chain A: D.358, L.359, N.362, C.372, Y.375, K.379, E.382 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.379 P6G.8: 7 residues within 4Å: Chain A: D.48, Y.52, E.64, K.67, E.75, K.76, A.79 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.67, A:E.75 Hydrogen bonds: A:K.76

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.9: 10 residues within 4Å: Chain A: A.98, R.101, L.102, F.105, L.206, L.207, D.246, C.249, E.250 Ligands: EDO.19 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.101 PG4.10: 15 residues within 4Å: Chain A: F.153, P.155, T.156, Q.199, I.221, L.222, K.225, V.241, N.244, Y.245, T.260, V.263, M.264, Q.291, I.294 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.156, A:T.156, A:Q.199, A:Q.291, A:Q.291

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.11: 6 residues within 4Å: Chain A: D.327, F.330, L.350, V.353, Q.354, K.357 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.350, A:K.357 PGE.12: 4 residues within 4Å: Chain A: H.163, V.167, V.188, Y.191 No protein-ligand interaction detected (PLIP)

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.13: 2 residues within 4Å: Chain A: K.558, K.561 No protein-ligand interaction detected (PLIP) PEG.14: 5 residues within 4Å: Chain A: I.221, Q.224, K.225, K.298 Ligands: PG6.17 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.221, A:K.225 PEG.15: 2 residues within 4Å: Chain A: K.232, E.233 No protein-ligand interaction detected (PLIP) PEG.16: 5 residues within 4Å: Chain A: K.525, T.526, F.529, A.553, V.556 No protein-ligand interaction detected (PLIP)

1 x PG6: 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE(Non-covalent)

PG6.17: 12 residues within 4Å: Chain A: Y.198, H.201, I.346, P.347, L.350, A.448, C.449, N.452, L.453, D.455, F.482 Ligands: PEG.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.452

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

EDO.18: 3 residues within 4Å: Chain A: S.170, E.173, E.174 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.174 EDO.19: 1 residues within 4Å: Ligands: PG4.9 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.101

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Naschberger, A. et al., Controlled dehydration, structural flexibility and gadolinium MRI contrast compound binding in the human plasma glycoprotein afamin. Acta Crystallogr D Struct Biol (2019)

Release Date

2019-01-02

Peptides

Afamin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Afamin

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