SMTL ID : 4rh7.1

Crystal structure of human cytoplasmic dynein 2 motor domain in complex with ADP.Vi

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.41 Å

Oligo State

monomer

Ligands

1 x AOV: ADP ORTHOVANADATE

AOV.1: 24 residues within 4Å: Chain A: L.804, V.805, P.832, A.833, G.834, T.835, G.836, K.837, T.838, E.839, D.883, E.884, T.932, N.934, I.967, L.1008, R.1009, K.1012, N.1209, D.1213, D.1214, A.1247, R.1251 Ligands: MG.2 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:V.805, A:V.805, A:G.834, A:T.835, A:G.836, A:K.837, A:K.837, A:T.838, A:E.839, A:D.883, A:T.932, A:N.934, A:R.1009, A:R.1009, A:K.1012, A:D.1213, A:D.1214, A:R.1251 Salt bridges: A:K.837, A:R.1009, A:R.1009

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: T.838, D.883, E.884, D.1213, R.1251 Ligands: AOV.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.838, A:D.883, A:D.883 MG.4: 4 residues within 4Å: Chain A: S.1128, D.1197, E.1237 Ligands: ATP.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.1128, A:E.1237

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

ATP.3: 17 residues within 4Å: Chain A: F.1089, Y.1094, E.1095, Q.1100, S.1123, G.1124, A.1125, G.1126, K.1127, S.1128, T.1129, E.1237, L.1267, S.1270, M.1315, R.1562 Ligands: MG.4 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:E.1095, A:E.1095, A:Q.1100, A:G.1124, A:G.1126, A:K.1127, A:S.1128, A:S.1128, A:S.1128, A:T.1129, A:S.1270 Salt bridges: A:K.1127, A:K.1127, A:R.1562

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

ADP.5: 18 residues within 4Å: Chain A: V.1404, I.1405, M.1410, E.1435, G.1436, C.1437, G.1438, K.1439, G.1440, M.1441, R.1444, K.1501, I.1583, Y.1584, Y.1587, P.1638, C.1639, T.1642 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:I.1405, A:I.1405, A:G.1436, A:G.1438, A:K.1439, A:G.1440, A:M.1441, A:R.1444 Salt bridges: A:K.1439, A:K.1501, A:K.1501 ADP.6: 15 residues within 4Å: Chain A: L.1767, D.1768, I.1769, L.1770, F.1772, R.1798, S.1799, G.1800, V.1801, G.1802, R.1803, R.1804, T.1805, E.1855, M.2015 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:L.1770, A:L.1770, A:G.1800, A:V.1801, A:G.1802, A:R.1803, A:R.1804, A:T.1805, A:T.1805, A:T.1805, A:E.1855 Salt bridges: A:R.1803, A:R.1804

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schmidt, H. et al., Structure of human cytoplasmic dynein-2 primed for its power stroke. Nature (2015)

Release Date

2014-12-10

Peptides

Green fluorescent protein/Cytoplasmic dynein 2 heavy chain 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Green fluorescent protein/Cytoplasmic dynein 2 heavy chain 1