SMTL ID : 4a5y.1

Intermediate state of human kinesin Eg5 in complex with Ispinesib

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-trimer

Ligands

3 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 12 residues within 4Å: Chain A: R.24, R.26, P.27, Q.106, T.107, G.108, T.109, G.110, K.111, T.112, F.113, E.118 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:R.24, A:G.108, A:T.109, A:G.110, A:K.111, A:T.112, A:T.112, A:F.113, A:E.118 Water bridges: A:R.24, A:R.24, A:R.24 pi-Stacking: A:F.113, A:F.113 ADP.4: 10 residues within 4Å: Chain B: R.24, R.26, P.27, T.107, G.108, G.110, K.111, T.112, F.113, E.118 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:R.24, B:R.24, B:T.107, B:G.108, B:G.110, B:K.111, B:T.112, B:F.113, B:E.118 Salt bridges: B:K.111 pi-Stacking: B:F.113, B:F.113 ADP.6: 13 residues within 4Å: Chain C: R.24, R.26, P.27, Q.106, T.107, G.108, T.109, G.110, K.111, T.112, F.113, E.118 Ligands: MG.7 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:R.24, C:Q.106, C:G.108, C:T.109, C:G.110, C:K.111, C:T.112, C:T.112, C:F.113 Water bridges: C:R.24, C:R.24, C:R.24, C:T.107, C:K.111 Salt bridges: C:K.111 pi-Stacking: C:F.113, C:F.113

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

CL.2: 2 residues within 4Å: Chain A: H.141, K.207 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: K.197, G.198 Chain C: K.197, G.198 Ligand excluded by PLIP

3 x G7X: ISPINESIB MESILATE(Non-covalent)

G7X.3: 17 residues within 4Å: Chain A: T.112, E.116, G.117, E.118, R.119, W.127, D.130, A.133, I.136, P.137, L.160, Y.211, L.214, E.215, G.217, A.218, R.221 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:E.116, A:R.119, A:W.127, A:W.127, A:W.127, A:D.130, A:A.133, A:P.137, A:L.160, A:Y.211, A:L.214, A:L.214, A:E.215, A:A.218 Hydrogen bonds: A:E.116, A:E.116, A:R.221 G7X.5: 18 residues within 4Å: Chain B: T.112, E.116, G.117, E.118, R.119, W.127, D.130, A.133, I.136, P.137, L.160, V.210, Y.211, L.214, E.215, G.217, A.218, R.221 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:E.116, B:R.119, B:W.127, B:W.127, B:W.127, B:D.130, B:A.133, B:I.136, B:P.137, B:L.160, B:V.210, B:Y.211, B:L.214, B:L.214, B:L.214, B:A.218 Hydrogen bonds: B:E.116, B:E.116 G7X.11: 16 residues within 4Å: Chain C: E.116, G.117, E.118, R.119, W.127, D.130, A.133, I.136, P.137, L.160, Y.211, L.214, E.215, G.217, A.218, R.221 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:W.127, C:W.127, C:D.130, C:A.133, C:P.137, C:P.137, C:L.160, C:Y.211, C:Y.211, C:L.214, C:L.214, C:A.218 Hydrogen bonds: C:E.116, C:E.116 Water bridges: C:G.117, C:R.221

1 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 3 residues within 4Å: Chain C: T.112, D.265 Ligands: ADP.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.112

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

PO4.8: 7 residues within 4Å: Chain B: E.129, H.141, E.145, K.207 Chain C: D.186, R.312, R.318 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:E.145, B:E.145, C:D.186 Salt bridges: B:H.141, B:K.207, C:R.318 Water bridges: C:D.186, C:D.186 PO4.9: 1 residues within 4Å: Chain C: R.53 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kaan, H.Y.K. et al., Snapshots" of Ispinesib-Induced Conformational Changes in the Mitotic Kinesin Eg5. J.Biol.Chem. (2013)

Release Date

2012-11-07

Peptides

KINESIN-LIKE PROTEIN KIF11: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

KINESIN-LIKE PROTEIN KIF11

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