SMTL ID : 5z0b.1

Crystal structure of plasma-derived human serum albumin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

homo-trimer

Ligands

3 x EIC: LINOLEIC ACID(Non-covalent)

EIC.1: 10 residues within 4Å: Chain A: K.195, L.198, K.199, F.211, W.214, A.215, D.451, Y.452, V.455 Ligands: SO4.7 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:K.195, A:K.195, A:L.198, A:K.199, A:K.199, A:F.211, A:F.211, A:W.214, A:W.214, A:W.214, A:A.215, A:D.451, A:Y.452, A:V.455 Water bridges: A:R.222 Salt bridges: A:K.199 EIC.20: 10 residues within 4Å: Chain B: K.195, L.198, K.199, F.211, W.214, A.215, D.451, Y.452, V.455 Ligands: SO4.25 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:K.195, B:L.198, B:K.199, B:F.211, B:F.211, B:W.214, B:W.214, B:A.215, B:D.451, B:Y.452, B:V.455 Salt bridges: B:K.199 EIC.43: 10 residues within 4Å: Chain C: K.195, L.198, K.199, F.211, W.214, A.215, D.451, Y.452, V.455 Ligands: SO4.49 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:K.195, C:L.198, C:K.199, C:F.211, C:W.214, C:W.214, C:A.215, C:D.451, C:Y.452, C:V.455 Salt bridges: C:K.199

5 x OCA: OCTANOIC ACID (CAPRYLIC ACID)(Non-covalent)

OCA.2: 9 residues within 4Å: Chain A: V.46, L.69, F.70, K.73, G.248, D.249, L.250, L.251, E.252 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.46, A:L.69, A:F.70, A:K.73, A:L.251 Hydrogen bonds: A:L.250, A:L.251 OCA.4: 5 residues within 4Å: Chain A: A.213, L.327, A.350, K.351, E.354 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.327, A:A.350 Hydrogen bonds: A:A.350 Water bridges: A:R.209, A:R.209, A:K.351 Salt bridges: A:R.209, A:K.351 OCA.21: 7 residues within 4Å: Chain B: V.46, L.69, F.70, K.73, G.248, L.250, L.251 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.69, B:F.70, B:K.73, B:L.251 Hydrogen bonds: B:L.250, B:L.251 OCA.44: 12 residues within 4Å: Chain C: A.26, V.46, L.66, L.69, F.70, K.73, G.248, D.249, L.250, L.251, E.252 Ligands: PEG.55 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:A.26, C:V.46, C:V.46, C:L.66, C:L.69, C:K.73, C:L.251 Hydrogen bonds: C:L.250, C:L.251 OCA.46: 6 residues within 4Å: Chain C: K.212, A.213, L.327, A.350, K.351, E.354 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:K.212, C:L.327, C:A.350 Water bridges: C:R.209, C:R.209, C:K.351 Salt bridges: C:R.209, C:K.351

4 x PLM: PALMITIC ACID(Non-covalent)

PLM.3: 9 residues within 4Å: Chain A: Y.138, I.142, R.145, H.146, Y.161, L.185, R.186, G.189, K.190 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.142, A:Y.161, A:Y.161, A:L.185, A:K.190 Salt bridges: A:R.114, A:H.146, A:R.186 PLM.22: 11 residues within 4Å: Chain B: R.114, Y.138, I.142, R.145, H.146, F.149, Y.161, L.185, R.186, G.189, K.190 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.142, B:I.142, B:F.149, B:Y.161, B:L.185, B:K.190 Salt bridges: B:R.114, B:H.146, B:R.186, B:K.190 PLM.23: 11 residues within 4Å: Chain B: R.209, K.212, A.213, V.216, D.324, V.325, L.327, G.328, A.350, K.351, E.354 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:K.212, B:V.216, B:V.325, B:L.327, B:A.350 Water bridges: B:R.209, B:R.209, B:K.351 Salt bridges: B:R.209, B:K.351 PLM.45: 11 residues within 4Å: Chain C: Y.138, I.142, H.146, F.149, F.157, Y.161, L.182, L.185, R.186, G.189, K.190 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:I.142, C:I.142, C:F.149, C:F.157, C:Y.161, C:L.185, C:R.186 Salt bridges: C:H.146, C:K.190

3 x TRP: TRYPTOPHAN(Non-covalent)

TRP.5: 11 residues within 4Å: Chain A: L.387, N.391, F.403, L.407, R.410, Y.411, L.430, V.433, G.434, L.453, S.489 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:N.391, A:V.433, A:L.453 Hydrogen bonds: A:Y.411, A:Y.411, A:L.430, A:S.489 Salt bridges: A:R.410, A:K.414 TRP.24: 11 residues within 4Å: Chain B: L.387, N.391, F.403, L.407, R.410, Y.411, L.430, V.433, G.434, L.453, S.489 11 PLIP interactions: 11 interactions with chain B, Hydrophobic interactions: B:N.391, B:F.403, B:V.433, B:L.453, B:L.453 Hydrogen bonds: B:Y.411, B:Y.411, B:L.430, B:S.489 Salt bridges: B:R.410, B:K.414 TRP.47: 11 residues within 4Å: Chain C: L.387, N.391, F.403, L.407, R.410, Y.411, L.430, V.433, G.434, L.453, S.489 9 PLIP interactions: 9 interactions with chain C, Hydrophobic interactions: C:N.391, C:F.403, C:V.433 Hydrogen bonds: C:Y.411, C:Y.411, C:Y.411, C:L.430 Salt bridges: C:R.410, C:K.414

19 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 4 residues within 4Å: Chain A: R.186, K.190, R.428, K.432 Ligand excluded by PLIP SO4.7: 7 residues within 4Å: Chain A: Y.150, K.199, L.238, H.242, R.257, A.291 Ligands: EIC.1 Ligand excluded by PLIP SO4.8: 6 residues within 4Å: Chain A: Q.417, V.469, S.470, D.471, R.472, D.494 Ligand excluded by PLIP SO4.9: 5 residues within 4Å: Chain A: V.418, S.419, T.420, K.500, K.534 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain A: G.399, E.400, Y.401 Ligand excluded by PLIP SO4.11: 6 residues within 4Å: Chain A: F.206, K.351, S.480, L.481, V.482 Ligands: PEG.17 Ligand excluded by PLIP SO4.12: 5 residues within 4Å: Chain A: D.121, A.172, D.173, K.174, A.175 Ligand excluded by PLIP SO4.13: 4 residues within 4Å: Chain A: K.413, T.540, K.541, E.542 Ligand excluded by PLIP SO4.25: 7 residues within 4Å: Chain B: Y.150, K.199, L.238, H.242, R.257, A.291 Ligands: EIC.20 Ligand excluded by PLIP SO4.26: 5 residues within 4Å: Chain B: Q.417, S.470, D.471, R.472, D.494 Ligand excluded by PLIP SO4.27: 4 residues within 4Å: Chain B: S.419, T.420, K.500, K.534 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain B: G.399, E.400, Y.401 Ligand excluded by PLIP SO4.29: 4 residues within 4Å: Chain B: R.186, K.190, R.428, K.432 Ligand excluded by PLIP SO4.30: 6 residues within 4Å: Chain B: F.206, K.351, S.480, L.481, V.482 Ligands: PEG.35 Ligand excluded by PLIP SO4.31: 2 residues within 4Å: Chain B: T.540, K.541 Ligand excluded by PLIP SO4.48: 6 residues within 4Å: Chain C: F.206, K.351, S.480, L.481, V.482 Ligands: PEG.52 Ligand excluded by PLIP SO4.49: 7 residues within 4Å: Chain C: Y.150, K.199, L.238, H.242, R.257, A.291 Ligands: EIC.43 Ligand excluded by PLIP SO4.50: 5 residues within 4Å: Chain C: Q.417, S.470, D.471, R.472, T.496 Ligand excluded by PLIP SO4.51: 4 residues within 4Å: Chain C: S.304, L.305, A.306, R.337 Ligand excluded by PLIP

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

PEG.14: 4 residues within 4Å: Chain A: A.194, N.429, K.432, Y.452 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.429 Water bridges: A:A.191 PEG.17: 5 residues within 4Å: Chain A: R.348, T.352, L.380, N.483 Ligands: SO4.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.480, A:S.480, A:N.483 PEG.19: 4 residues within 4Å: Chain A: K.225, D.269, S.270, I.271 No protein-ligand interaction detected (PLIP) PEG.32: 3 residues within 4Å: Chain B: F.134, K.137, Y.161 No protein-ligand interaction detected (PLIP) PEG.33: 5 residues within 4Å: Chain B: N.429, K.432, Y.452, V.456, Q.459 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.429, B:Q.459 PEG.35: 7 residues within 4Å: Chain B: R.348, K.351, T.352, L.380, S.480, N.483 Ligands: SO4.30 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.480, B:N.483 PEG.36: 2 residues within 4Å: Chain B: S.58, D.63 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.58, B:D.63 PEG.38: 3 residues within 4Å: Chain B: R.209, E.354 Ligands: 1PE.41 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.209, B:E.354 PEG.39: 3 residues within 4Å: Chain B: T.356, C.369, E.376 No protein-ligand interaction detected (PLIP) PEG.40: 5 residues within 4Å: Chain B: Y.334, Y.341, F.374, F.377, K.378 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.334 PEG.52: 5 residues within 4Å: Chain C: R.348, T.352, S.480, N.483 Ligands: SO4.48 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.480, C:N.483 PEG.55: 6 residues within 4Å: Chain C: E.45, N.61, L.69, D.72, K.73 Ligands: OCA.44 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.45, C:K.73 PEG.57: 6 residues within 4Å: Chain C: H.146, K.190, S.193, A.194, R.197, Q.459 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.190, C:Q.459

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

PGE.15: 4 residues within 4Å: Chain A: E.277, E.280, K.281 Chain C: M.298 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Water bridges: C:M.298 Hydrogen bonds: A:K.281 PGE.34: 6 residues within 4Å: Chain B: K.233, D.237, D.256, D.259, L.260, Y.263 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.233, B:K.233, B:D.259 PGE.42: 4 residues within 4Å: Chain B: T.243, E.244, H.247, D.249 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.244 PGE.53: 6 residues within 4Å: Chain B: E.297 Chain C: K.225, Q.268, D.269, S.270, I.271 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.225

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

PG4.16: 4 residues within 4Å: Chain A: E.208, T.243, H.247, D.249 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.249 PG4.18: 4 residues within 4Å: Chain A: A.320, K.323, E.358, C.361 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.323, A:E.358, A:E.358 Water bridges: A:E.358 PG4.37: 7 residues within 4Å: Chain A: E.297 Chain B: K.225, D.269, S.270, I.271, S.272, S.273 No protein-ligand interaction detected (PLIP) PG4.54: 3 residues within 4Å: Chain C: Y.319, A.320, K.323 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.323 PG4.56: 4 residues within 4Å: Chain C: T.243, E.244, H.247, D.249 2 PLIP interactions: 2 interactions with chain C Water bridges: C:E.208, C:K.240

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.41: 5 residues within 4Å: Chain B: Y.319, K.323, E.358, C.361 Ligands: PEG.38 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.323, B:E.358

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, J. et al., The crystal structure of plasma-derived human serum albumin. To Be Published

Release Date

2018-12-19

Peptides

Serum albumin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Serum albumin

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