SMTL ID : 4dbp.1

Myosin VI nucleotide-free (MDINSERT2) D179Y crystal structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-mer

Ligands

2 x TBU: TERTIARY-BUTYL ALCOHOL(Non-functional Binders)

TBU.1: 8 residues within 4Å: Chain A: R.204, F.205, G.206, L.228, E.230, I.456, I.472, F.646 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.456, A:F.646 Hydrogen bonds: A:L.228 TBU.2: 6 residues within 4Å: Chain A: T.157, T.160, K.161, L.164, N.185, K.207 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.157, A:K.161, A:L.164, A:N.185 Water bridges: A:I.181, A:N.185

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

EDO.3: 7 residues within 4Å: Chain A: M.65, M.716, Y.717, K.719, Y.720, D.766, K.770 Ligand excluded by PLIP EDO.4: 7 residues within 4Å: Chain A: N.283, K.284, D.287, Y.299, G.303, S.304, K.306 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: L.142, R.486, R.658, T.660 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: Y.99, K.669, L.672, M.674 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: K.549, H.550, D.552, H.553 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: V.6, V.47, F.48, P.49 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: K.141, L.142, S.143, S.448 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: R.555, H.580, F.581 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: P.49, Y.66, L.67, N.68, P.759, G.760 Ligand excluded by PLIP EDO.12: 8 residues within 4Å: Chain A: A.252, G.253, A.254, Q.289, I.290, L.291, R.294, H.313 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: D.268, N.274, T.278, E.298 Ligand excluded by PLIP EDO.14: 8 residues within 4Å: Chain A: T.196, V.197, R.204, E.241, E.460, F.462, Q.469, I.472 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: L.229, E.230, K.231, S.232, V.642, F.646 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain A: E.504, V.505, H.506 Ligand excluded by PLIP EDO.17: 9 residues within 4Å: Chain A: T.168, G.172, T.173, G.174, Q.175, D.176, I.177, Y.178, V.219 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain A: E.230, S.232, R.233, V.236, Q.237, E.468 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: K.497, G.499 Chain B: F.66, P.67 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain A: F.48, N.68, E.69, L.697, D.698, Q.701 Ligand excluded by PLIP

1 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.21: 8 residues within 4Å: Chain A: S.149, N.476, L.479, Q.480, F.483, F.581, R.666, S.691 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.476, A:L.479, A:F.581 Hydrogen bonds: A:R.666

4 x CA: CALCIUM ION(Non-covalent)

CA.22: 5 residues within 4Å: Chain B: D.21, D.23, D.25, T.27, E.32 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.25, B:T.27, B:E.32, B:E.32, H2O.29 CA.23: 5 residues within 4Å: Chain B: D.57, D.59, N.61, T.63, E.68 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.57, B:D.59, B:T.63, B:E.68 CA.24: 5 residues within 4Å: Chain B: D.94, D.96, N.98, F.100, E.105 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.94, B:F.100 CA.25: 6 residues within 4Å: Chain B: D.130, D.132, D.134, Q.136, V.137, E.141 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:Q.136, B:E.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Song, L. et al., Mutations in myosin VI that cause a loss of coordination between heads provide insights into the structural changes underlying force generation and the importance of gating. To be Published

Release Date

2013-01-30

Peptides

Myosin-VI: A
Calmodulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Myosin-VI

Calmodulin

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