SMTL ID : 8k1y.1

Crystal structure of human serum albumin and ruthenium Val complex adduct

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

1 x NO: NITRIC OXIDE(Non-covalent)

NO.1: 4 residues within 4Å: Chain A: H.146 Ligands: VAL.2, CL.3, RU.4 No protein-ligand interaction detected (PLIP)

1 x VAL: VALINE(Non-covalent)

VAL.2: 9 residues within 4Å: Chain A: H.146, F.149, L.154, Y.161, G.189, K.190 Ligands: NO.1, CL.3, RU.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:F.149, A:K.190 Hydrogen bonds: A:Y.161, A:Y.161, V.2

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

CL.3: 4 residues within 4Å: Ligands: NO.1, VAL.2, RU.4, PLM.10 Ligand excluded by PLIP

1 x RU: RUTHENIUM ION(Non-functional Binders)

RU.4: 3 residues within 4Å: Ligands: NO.1, VAL.2, CL.3 No protein-ligand interaction detected (PLIP)

6 x PLM: PALMITIC ACID(Non-covalent)

PLM.5: 13 residues within 4Å: Chain A: S.342, V.344, R.348, P.384, L.387, I.388, N.391, L.430, C.437, C.438, A.449, R.485 Ligands: PLM.8 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.384, A:L.387, A:I.388, A:A.449 Hydrogen bonds: A:S.342 Salt bridges: A:R.348, A:R.485 PLM.6: 15 residues within 4Å: Chain A: Y.401, N.405, F.502, F.507, K.525, A.528, L.529, L.532, V.547, M.548, F.551, A.552, L.575, S.579, Q.580 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.401, A:F.502, A:F.507, A:F.507, A:F.507, A:A.528, A:L.532, A:V.547, A:M.548, A:F.551, A:L.575, A:Q.580 Salt bridges: A:K.525 PLM.7: 15 residues within 4Å: Chain A: R.10, L.14, L.22, V.23, V.46, L.66, F.70, Y.150, L.251, A.254, R.257, A.258, L.283, L.284, S.287 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.14, A:L.22, A:V.23, A:V.46, A:L.66, A:L.251, A:A.254, A:L.283, A:L.284 Hydrogen bonds: A:S.287 Water bridges: A:S.287, A:H.288 Salt bridges: A:R.257 PLM.8: 13 residues within 4Å: Chain A: L.387, R.410, Y.411, V.418, T.422, L.453, L.460, L.463, H.464, V.473, F.488, S.489 Ligands: PLM.5 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.411, A:Y.411, A:Y.411, A:V.418, A:V.418, A:T.422, A:L.453, A:L.460, A:L.460, A:L.463, A:H.464, A:V.473, A:V.473, A:F.488 Hydrogen bonds: A:R.410, A:Y.411, A:S.489 Salt bridges: A:K.414 PLM.9: 15 residues within 4Å: Chain A: R.209, A.210, A.213, V.216, F.228, S.232, D.324, L.327, G.328, L.347, A.350, K.351, E.354, S.480, V.482 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.213, A:V.216, A:F.228, A:D.324, A:L.327, A:A.350, A:K.351 Hydrogen bonds: A:S.480 Salt bridges: A:K.351 PLM.10: 9 residues within 4Å: Chain A: R.117, L.135, K.136, Y.138, L.155, A.158, K.159, Y.161 Ligands: CL.3 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.135, A:L.135, A:Y.138, A:Y.138, A:Y.138, A:L.155, A:A.158, A:Y.161, A:Y.161, A:Y.161, A:Y.161 Water bridges: A:R.117 Salt bridges: A:R.117

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 6 residues within 4Å: Chain A: K.199, R.218, L.219, R.222, L.238, A.291 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.199, A:K.199, A:R.222 GOL.12: 7 residues within 4Å: Chain A: Y.30, H.67, F.70, N.99, D.249, L.250, L.251 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.30, A:Y.30, A:D.249, A:L.250, A:L.251

4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.13: 5 residues within 4Å: Chain A: K.199, S.202, F.211, W.214, L.481 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.202 pi-Cation interactions: A:W.214 DMS.14: 5 residues within 4Å: Chain A: Q.33, C.34, V.77, T.79, T.83 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.38 DMS.15: 6 residues within 4Å: Chain A: K.106, Y.148, Y.150, C.245, G.248, L.250 No protein-ligand interaction detected (PLIP) DMS.16: 4 residues within 4Å: Chain A: E.6, S.65, L.66, H.67 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.65 Salt bridges: A:E.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gong, W.J. et al., Crystal structure of human serum albumin and ruthenium VaL complex adduct. To Be Published

Release Date

2024-07-17

Peptides

Albumin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Albumin

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