SMTL ID : 6asy.1

BiP-ATP2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 2 residues within 4Å: Chain A: K.330, N.357 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.357, A:N.357 Water bridges: A:K.330 GOL.2: 4 residues within 4Å: Chain A: G.35, N.36, R.37, I.38 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.35, A:R.37, A:R.37, A:I.38 Water bridges: A:D.368 GOL.3: 5 residues within 4Å: Chain A: E.335, S.362, R.363 Chain B: R.26, V.27 11 PLIP interactions: 4 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:R.26, A:S.362, A:R.363, A:R.363 Water bridges: B:R.26, B:Y.373, B:Y.373, A:K.190, A:K.190, A:E.192, A:E.335 GOL.4: 3 residues within 4Å: Chain A: E.50, L.528, R.535 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.50, A:R.535, A:R.535 GOL.5: 3 residues within 4Å: Chain A: M.316, K.317, Q.320 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.317, A:Q.320 Water bridges: A:R.313 GOL.17: 4 residues within 4Å: Chain B: G.35, N.36, R.37, I.38 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.35, B:R.37, B:R.37, B:I.38 Water bridges: B:R.37, B:E.369 GOL.18: 3 residues within 4Å: Chain B: E.50, L.528, R.535 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.50, B:R.535, B:R.535 GOL.19: 2 residues within 4Å: Chain B: K.330, N.357 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.357 Water bridges: B:K.330, B:F.355

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.6: 23 residues within 4Å: Chain A: D.11, G.13, T.14, T.15, Y.16, K.73, E.178, G.203, G.204, G.205, T.206, G.232, E.270, K.273, R.274, S.277, G.340, G.341, S.342, R.344, I.345, P.367, D.368 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:T.14, A:T.15, A:Y.16, A:Y.16, A:E.178, A:G.203, A:G.204, A:G.205, A:T.206, A:T.206, A:E.270, A:K.273, A:R.274, A:S.277, A:G.341, A:R.344 Water bridges: A:Y.16, A:K.73, A:K.73, A:T.206, A:T.206, A:R.274, A:R.274, A:R.274 Salt bridges: A:K.73 ATP.20: 23 residues within 4Å: Chain B: D.11, G.13, T.14, T.15, Y.16, K.73, E.178, G.203, G.204, G.205, T.206, G.232, E.270, K.273, R.274, S.277, G.340, G.341, S.342, R.344, I.345, P.367, D.368 28 PLIP interactions: 28 interactions with chain B Hydrogen bonds: B:T.14, B:T.14, B:T.15, B:Y.16, B:Y.16, B:E.178, B:G.203, B:G.204, B:G.205, B:T.206, B:T.206, B:E.270, B:K.273, B:R.274, B:S.277, B:G.341, B:R.344, B:D.368 Water bridges: B:D.11, B:K.73, B:K.73, B:E.178, B:E.178, B:E.178, B:E.178, B:P.367, B:D.368 Salt bridges: B:K.73

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

SO4.7: 4 residues within 4Å: Chain A: R.363, G.364 Chain B: R.37, N.366 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:G.364, B:N.366 Water bridges: A:I.365, B:R.37, B:G.364, B:N.366 Salt bridges: B:R.37 SO4.8: 3 residues within 4Å: Chain A: H.242, K.303, L.307 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.242, A:K.303 SO4.9: 5 residues within 4Å: Chain A: K.253, D.254, K.257, Y.290, E.291 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.290, A:E.291 Water bridges: A:D.254, A:K.257 Salt bridges: A:K.253, A:K.257 SO4.10: 3 residues within 4Å: Chain A: Q.279, H.280, Q.281 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.280, A:Q.281 SO4.21: 5 residues within 4Å: Chain A: R.37, N.366 Chain B: R.363, G.364 Ligands: PO4.16 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:N.366, A:E.369, B:G.364 Water bridges: A:R.37, B:R.363, B:I.365, B:I.365 Salt bridges: A:R.37, B:R.363 SO4.22: 4 residues within 4Å: Chain B: D.254, K.257, Y.290, E.291 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.290 Water bridges: B:D.254, B:E.291, B:E.291 Salt bridges: B:K.253, B:K.257 SO4.23: 3 residues within 4Å: Chain B: Q.279, H.280, Q.281 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.280, B:Q.281 SO4.24: 3 residues within 4Å: Chain B: H.242, K.303, L.307 4 PLIP interactions: 4 interactions with chain B Water bridges: B:H.242, B:K.245 Salt bridges: B:H.242, B:K.303

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

PO4.11: 6 residues within 4Å: Chain A: D.71, R.74, D.88, F.91, E.233, D.234 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.88, A:D.234 Salt bridges: A:R.74 PO4.12: 1 residues within 4Å: Chain A: K.321 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.321, A:K.321, A:K.321 Salt bridges: A:K.321 PO4.13: 3 residues within 4Å: Chain A: R.443, P.444, D.448 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.443, A:D.448 Salt bridges: A:R.443 PO4.14: 2 residues within 4Å: Chain A: Q.159, K.162 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.159 Water bridges: A:D.163, A:T.166 Salt bridges: A:K.162 PO4.15: 5 residues within 4Å: Chain A: E.2, V.4, H.144, N.171, M.173 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.171 Water bridges: A:E.2, A:E.2, A:H.144 Salt bridges: A:H.144 PO4.16: 5 residues within 4Å: Chain A: G.364, I.365, N.366, A.370 Ligands: SO4.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.364, A:N.366 PO4.25: 6 residues within 4Å: Chain B: D.71, R.74, D.88, F.91, E.233, D.234 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.71, B:D.88, B:E.233 Water bridges: B:D.234 Salt bridges: B:R.74 PO4.26: 5 residues within 4Å: Chain B: E.2, V.4, H.144, N.171, M.173 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.171, B:N.171 Water bridges: B:E.2, B:N.171, B:N.171 Salt bridges: B:H.144 PO4.27: 2 residues within 4Å: Chain B: Q.159, K.162 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.159 Water bridges: B:R.483, B:R.483 Salt bridges: B:K.162 PO4.28: 4 residues within 4Å: Chain A: R.26 Chain B: E.335, S.362, R.363 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.363 Water bridges: B:Y.186, B:K.190, B:R.363, A:R.26, A:R.26 Salt bridges: B:K.190, A:R.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, J. et al., Conformation transitions of the polypeptide-binding pocket support an active substrate release from Hsp70s. Nat Commun (2017)

Release Date

2017-12-06

Peptides

78 kDa glucose-regulated protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

78 kDa glucose-regulated protein

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