SMTL ID : 3nwn.1

Crystal structure of the human KIF9 motor domain in complex with ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-trimer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: T.119 Ligands: ADP.3 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.119, H2O.1, H2O.1, H2O.1, H2O.1 MG.12: 2 residues within 4Å: Chain B: T.119 Ligands: ADP.14 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:T.119, H2O.4, H2O.4, H2O.4, H2O.4 MG.23: 2 residues within 4Å: Chain C: T.119 Ligands: ADP.25 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:T.119, H2O.7, H2O.7, H2O.7, H2O.7

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

CL.2: 3 residues within 4Å: Chain A: S.84, Q.85, H.131 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain B: S.84, Q.85, H.131 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain C: S.84, Q.85, H.131 Ligand excluded by PLIP

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

ADP.3: 12 residues within 4Å: Chain A: R.31, K.33, P.34, Q.113, T.114, G.115, A.116, G.117, K.118, T.119, Y.120 Ligands: MG.1 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:R.31, A:G.115, A:A.116, A:G.117, A:K.118, A:T.119, A:T.119, A:Y.120 Water bridges: A:R.31, A:R.31, A:T.114, A:K.118, A:K.118, A:T.119 Salt bridges: A:K.118 ADP.14: 12 residues within 4Å: Chain B: R.31, K.33, P.34, Q.113, T.114, G.115, A.116, G.117, K.118, T.119, Y.120 Ligands: MG.12 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:R.31, B:G.115, B:A.116, B:G.117, B:K.118, B:T.119, B:T.119, B:Y.120 Water bridges: B:R.31, B:R.31, B:T.114, B:K.118, B:K.118, B:T.119 Salt bridges: B:K.118 ADP.25: 12 residues within 4Å: Chain C: R.31, K.33, P.34, Q.113, T.114, G.115, A.116, G.117, K.118, T.119, Y.120 Ligands: MG.23 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:R.31, C:G.115, C:A.116, C:G.117, C:K.118, C:T.119, C:T.119, C:Y.120 Water bridges: C:R.31, C:R.31, C:T.114, C:K.118, C:K.118, C:T.119 Salt bridges: C:K.118

24 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.4: 4 residues within 4Å: Chain A: N.190, Q.192 Chain B: G.179, M.228 Ligand excluded by PLIP UNX.5: 2 residues within 4Å: Chain A: D.86, R.132 Ligand excluded by PLIP UNX.6: 2 residues within 4Å: Chain A: H.152, A.153 Ligand excluded by PLIP UNX.7: 5 residues within 4Å: Chain A: A.153, I.154, T.155, E.244, H.246 Ligand excluded by PLIP UNX.8: 6 residues within 4Å: Chain A: S.159, Y.160, L.161, L.199, I.238, T.240 Ligand excluded by PLIP UNX.9: 5 residues within 4Å: Chain A: E.90, T.91, A.93, K.94, D.95 Ligand excluded by PLIP UNX.10: 3 residues within 4Å: Chain A: F.143, Q.206, E.207 Ligand excluded by PLIP UNX.11: 5 residues within 4Å: Chain A: E.162, S.225, K.230, S.232, S.235 Ligand excluded by PLIP UNX.15: 4 residues within 4Å: Chain B: N.190, Q.192 Chain C: G.179, M.228 Ligand excluded by PLIP UNX.16: 2 residues within 4Å: Chain B: D.86, R.132 Ligand excluded by PLIP UNX.17: 2 residues within 4Å: Chain B: H.152, A.153 Ligand excluded by PLIP UNX.18: 5 residues within 4Å: Chain B: A.153, I.154, T.155, E.244, H.246 Ligand excluded by PLIP UNX.19: 6 residues within 4Å: Chain B: S.159, Y.160, L.161, L.199, I.238, T.240 Ligand excluded by PLIP UNX.20: 5 residues within 4Å: Chain B: E.90, T.91, A.93, K.94, D.95 Ligand excluded by PLIP UNX.21: 3 residues within 4Å: Chain B: F.143, Q.206, E.207 Ligand excluded by PLIP UNX.22: 5 residues within 4Å: Chain B: E.162, S.225, K.230, S.232, S.235 Ligand excluded by PLIP UNX.26: 4 residues within 4Å: Chain A: G.179, M.228 Chain C: N.190, Q.192 Ligand excluded by PLIP UNX.27: 2 residues within 4Å: Chain C: D.86, R.132 Ligand excluded by PLIP UNX.28: 2 residues within 4Å: Chain C: H.152, A.153 Ligand excluded by PLIP UNX.29: 5 residues within 4Å: Chain C: A.153, I.154, T.155, E.244, H.246 Ligand excluded by PLIP UNX.30: 6 residues within 4Å: Chain C: S.159, Y.160, L.161, L.199, I.238, T.240 Ligand excluded by PLIP UNX.31: 5 residues within 4Å: Chain C: E.90, T.91, A.93, K.94, D.95 Ligand excluded by PLIP UNX.32: 3 residues within 4Å: Chain C: F.143, Q.206, E.207 Ligand excluded by PLIP UNX.33: 5 residues within 4Å: Chain C: E.162, S.225, K.230, S.232, S.235 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, H. et al., Crystal structure of the human KIF9 motor domain in complex with ADP. To be Published

Release Date

2010-07-21

Peptides

Kinesin-like protein KIF9: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Kinesin-like protein KIF9