SMTL ID : 8yhh.1

The Crystal Structure of Mitotic Kinesin Eg5 from Biortus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 14 residues within 4Å: Chain A: R.26, R.28, P.29, Q.108, T.109, G.110, T.111, G.112, K.113, T.114, F.115, E.120 Chain B: K.36 Ligands: MG.2 26 PLIP interactions: 24 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.26, A:G.110, A:T.111, A:T.111, A:G.112, A:K.113, A:T.114, A:F.115, A:E.120, B:K.36, B:K.36 Water bridges: A:R.26, A:R.26, A:R.26, A:K.113, A:T.114, A:T.114, A:T.114, A:T.114, A:T.114, A:T.114, A:T.114, A:D.267 Salt bridges: A:K.113 pi-Stacking: A:F.115, A:F.115 ADP.8: 14 residues within 4Å: Chain A: K.36 Chain B: R.26, R.28, P.29, Q.108, T.109, G.110, T.111, G.112, K.113, T.114, F.115, E.120 Ligands: MG.9 20 PLIP interactions: 19 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.26, B:G.110, B:T.111, B:G.112, B:K.113, B:T.114, B:F.115, B:E.120, A:K.36 Water bridges: B:R.26, B:R.26, B:R.26, B:K.113, B:T.114, B:T.114, B:T.114, B:D.267 Salt bridges: B:K.113 pi-Stacking: B:F.115, B:F.115

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: T.114 Ligands: ADP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.114, H2O.1, H2O.2, H2O.4, H2O.4 MG.9: 2 residues within 4Å: Chain B: T.114 Ligands: ADP.8 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:T.114, H2O.9, H2O.10, H2O.10, H2O.10

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

EDO.3: 5 residues within 4Å: Chain A: I.96, M.97, E.249, L.257, K.259 No protein-ligand interaction detected (PLIP) EDO.5: 8 residues within 4Å: Chain A: S.161, L.163, I.198, L.201, V.240, S.242, K.262, I.321 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.161, A:S.242, A:K.262, A:K.262 Water bridges: A:S.242 EDO.10: 5 residues within 4Å: Chain B: I.81, Y.84, R.85, R.140, Q.144 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.85, B:R.140 EDO.11: 3 residues within 4Å: Chain B: R.35, K.36, S.38 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.38 EDO.12: 7 residues within 4Å: Chain A: S.38, H.40 Chain B: T.224, A.227, Y.233, S.234 Ligands: EDO.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.224, B:S.234 EDO.13: 6 residues within 4Å: Chain B: S.161, L.163, V.240, S.242, K.262, I.321 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.161, B:S.161, B:S.242, B:K.262, B:I.321 Water bridges: B:S.242 EDO.14: 2 residues within 4Å: Chain B: L.59, K.62 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.62 EDO.15: 7 residues within 4Å: Chain A: A.39, S.342, L.343 Chain B: Y.233, S.234, S.235 Ligands: EDO.12 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.342, A:S.342, B:S.234, B:S.234, B:S.235

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.4: 1 residues within 4Å: Chain A: R.191 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: R.223, T.224, A.227, Y.233, S.234 Chain B: S.38, H.40 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.224, A:S.234, B:S.38 Water bridges: A:S.235

1 x NO3: NITRATE ION(Non-functional Binders)

NO3.7: 6 residues within 4Å: Chain A: Y.233, S.235, R.236 Chain B: A.39, S.342, L.343 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.236, A:R.236, B:S.342 Water bridges: A:S.235

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, F. et al., The Crystal Structure of Mitotic Kinesin Eg5 from Biortus. To Be Published

Release Date

2024-03-13

Peptides

Kinesin-like protein KIF11: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Kinesin-like protein KIF11