SMTL ID : 7gyk.1

Crystal Structure of HSP72 in complex with ligand 11 at 2.86 MGy X-ray dose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

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

PO4.1: 9 residues within 4Å: Chain A: G.17, T.18, K.76, P.152, E.180, T.209, D.211 Ligands: PO4.4, EDO.9 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:T.18, A:T.18, A:T.18, A:D.204, A:T.209 Water bridges: A:K.76, A:K.76, A:E.180, A:E.180, A:T.209 Salt bridges: A:K.76 PO4.2: 5 residues within 4Å: Chain A: M.92, W.95, P.96, F.97, Q.98 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:M.92, A:P.96, A:Q.98 Water bridges: A:V.99, A:V.99 PO4.3: 5 residues within 4Å: Chain A: Y.154, T.227, A.228, G.229, D.230 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.211, A:D.211, A:T.227 Water bridges: A:T.227, A:A.228, A:A.228, A:D.230 PO4.4: 8 residues within 4Å: Chain A: G.17, T.18, T.19, Y.20, G.206, G.207 Ligands: PO4.1, 01.15 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:T.18, A:T.19, A:T.19, A:Y.20, A:G.207 Water bridges: A:D.15, A:D.15, A:K.76, A:G.208

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

DMS.5: 4 residues within 4Å: Chain A: L.55, I.56, A.59, K.131 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.56 Water bridges: A:A.59 DMS.6: 5 residues within 4Å: Chain A: R.41, S.367, I.368, N.369, E.372 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.369 Water bridges: A:R.41 DMS.7: 3 residues within 4Å: Chain A: R.160, Q.161, I.177 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.161

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

EDO.8: 5 residues within 4Å: Chain A: R.347, K.366, S.367, N.369, P.370 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.347, A:R.347 Water bridges: A:S.367 EDO.9: 6 residues within 4Å: Chain A: T.18, K.76, R.77, Y.154, T.209 Ligands: PO4.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.18, A:R.77, A:Y.154 Water bridges: A:R.81, A:T.209 EDO.10: 4 residues within 4Å: Chain A: K.131, E.134, I.135, A.138 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.131, A:K.131, A:E.134, A:E.134 Water bridges: A:D.37 EDO.11: 3 residues within 4Å: Chain A: A.153, Y.154, F.155 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.154 Water bridges: A:R.160 EDO.12: 5 residues within 4Å: Chain A: K.164, V.168, L.172, N.173, V.174 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.172, A:V.174 Water bridges: A:N.173, A:V.174

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

PEG.13: 6 residues within 4Å: Chain A: R.176, I.177, I.178, N.179, T.182, Q.381 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.176, A:N.179, A:T.182 Water bridges: A:N.179

1 x 1PS: 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE(Non-covalent)

1PS.14: 2 residues within 4Å: Chain A: D.332, K.333 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.333 Water bridges: A:K.333, A:A.334, A:N.360 Salt bridges: A:K.333

1 x 01: 8-chloroadenosine

01.15: 12 residues within 4Å: Chain A: G.206, G.207, G.235, E.273, K.276, R.277, S.280, G.344, S.345, R.347, I.348 Ligands: PO4.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.276, A:R.277, A:S.280, A:G.344, A:R.347 Water bridges: A:R.347

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rodrigues, M.J. et al., Specific radiation damage to halogenated inhibitors and ligands in protein-ligand crystal structures. J.Appl.Crystallogr. (2024)

Release Date

2024-12-11

Peptides

Heat shock 70 kDa protein 1A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Heat shock 70 kDa protein 1A

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