SMTL ID : 4ai6.1

Dynein Motor Domain - ADP complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.40 Å

Oligo State

homo-dimer

Ligands

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

ATP.1: 22 residues within 4Å: Chain A: F.903, S.904, K.931, A.932, G.933, C.934, G.935, K.936, T.937, A.938, D.1011, E.1051, V.1075, C.1076, S.1080, K.1081, H.1084, R.1363, E.1367, R.1405, R.1408 Ligands: MG.10 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:S.904, A:S.904, A:G.933, A:C.934, A:G.935, A:K.936, A:T.937, A:T.937, A:A.938, A:H.1084, A:R.1405 Salt bridges: A:K.936, A:K.936, A:R.1363, A:R.1405, A:R.1408, A:R.1408, A:R.1408 pi-Stacking: A:F.903 pi-Cation interactions: A:K.1081 ATP.6: 22 residues within 4Å: Chain B: F.903, S.904, K.931, G.933, C.934, G.935, K.936, T.937, A.938, D.1011, E.1051, V.1075, C.1076, S.1080, K.1081, H.1084, R.1363, E.1367, R.1405, R.1408, H.1409 Ligands: MG.5 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:S.904, B:S.904, B:G.933, B:C.934, B:G.935, B:K.936, B:T.937, B:T.937, B:A.938, B:H.1084, B:R.1405 Salt bridges: B:K.936, B:K.936, B:R.1363, B:R.1405, B:R.1408, B:R.1408, B:R.1408 pi-Stacking: B:F.903

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

ADP.2: 17 residues within 4Å: Chain A: I.1246, V.1247, I.1248, T.1253, P.1275, P.1276, G.1277, S.1278, G.1279, K.1280, T.1281, M.1282, I.1426, Y.1427, P.1475, R.1476, T.1479 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:I.1248, A:I.1248, A:T.1253, A:P.1275, A:G.1277, A:S.1278, A:G.1279, A:K.1280, A:T.1281, A:T.1281, A:T.1281, A:M.1282 Salt bridges: A:K.1280, A:K.1280, A:R.1476, A:R.1476 ADP.3: 15 residues within 4Å: Chain A: P.1587, M.1588, V.1589, H.1591, M.1594, R.1619, T.1620, G.1621, K.1622, T.1623, I.1624, W.1776, I.1849, R.1853, R.2115 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:V.1589, A:V.1589, A:R.1619, A:R.1619, A:T.1620, A:G.1621, A:G.1621, A:K.1622, A:T.1623, A:I.1624, A:R.1853 Salt bridges: A:K.1622, A:R.2115, A:R.2115 pi-Cation interactions: A:R.1619 ADP.7: 16 residues within 4Å: Chain B: I.1246, I.1248, T.1250, P.1275, P.1276, G.1277, S.1278, G.1279, K.1280, T.1281, M.1282, I.1426, Y.1427, Y.1430, R.1476, T.1479 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:I.1248, B:I.1248, B:T.1250, B:G.1277, B:S.1278, B:G.1279, B:K.1280, B:T.1281, B:T.1281, B:T.1281, B:M.1282, B:T.1479 Salt bridges: B:K.1280, B:R.1476, B:R.1476 ADP.8: 13 residues within 4Å: Chain B: P.1587, M.1588, V.1589, H.1591, R.1619, T.1620, G.1621, K.1622, T.1623, I.1624, W.1776, R.1853, R.2115 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:V.1589, B:V.1589, B:H.1591, B:G.1616, B:R.1619, B:G.1621, B:K.1622, B:T.1623, B:T.1623, B:I.1624, B:R.1853 Salt bridges: B:K.1622, B:R.2115, B:R.2115 pi-Stacking: B:W.1776 pi-Cation interactions: B:R.1619

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 7 residues within 4Å: Chain A: A.654, G.655, T.656, G.657, K.658, T.659, E.705 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.655, A:T.656, A:T.656, A:G.657, A:K.658, A:T.659, A:T.659, A:E.705 Salt bridges: A:K.658 SO4.9: 8 residues within 4Å: Chain B: P.653, A.654, G.655, T.656, G.657, K.658, T.659, N.755 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.655, B:T.656, B:G.657, B:K.658, B:T.659, B:N.755 Salt bridges: B:K.658

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 6 residues within 4Å: Chain B: K.936, T.937, D.1011, E.1051, R.1405 Ligands: ATP.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:T.937, B:D.1011, B:E.1051 MG.10: 5 residues within 4Å: Chain A: T.937, D.1011, E.1051, E.1367 Ligands: ATP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.937, A:E.1367

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schmidt, H. et al., Insights Into Dynein Motor Domain Function from a 3.3 Angstrom Crystal Structure. Nat.Struct.Mol.Biol. (2012)

Release Date

2012-03-14

Peptides

GLUTATHIONE S-TRANSFERASE CLASS-MU 26 KDA ISOZYME, DYNEIN HEAVY CHAIN CYTOPLASMIC: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

GLUTATHIONE S-TRANSFERASE CLASS-MU 26 KDA ISOZYME, DYNEIN HEAVY CHAIN CYTOPLASMIC

Related Entries With Identical Sequence