SMTL ID : 4akg.1

Dynein Motor Domain - ATP complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.30 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.3 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:S.904, A:S.904, A:K.931, A:G.933, A:C.934, A:G.935, A:K.936, A:T.937, A:A.938, A:D.1011, A:E.1051, A:H.1084 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 ATP.6: 22 residues within 4Å: Chain B: F.903, S.904, K.931, A.932, G.933, C.934, G.935, K.936, T.937, A.938, E.1051, V.1075, C.1076, S.1080, K.1081, H.1084, L.1085, R.1363, E.1367, R.1405, R.1408 Ligands: MG.8 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:S.904, B:S.904, B:K.931, B:G.933, B:C.934, B:G.935, B:K.936, B:T.937, B:T.937, B:A.938, B:D.1011, 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

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

ADP.2: 18 residues within 4Å: Chain A: I.1246, V.1247, I.1248, T.1250, T.1253, P.1276, G.1277, S.1278, G.1279, K.1280, T.1281, M.1282, I.1426, Y.1427, Y.1430, P.1475, R.1476, T.1479 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:I.1248, A:I.1248, A:T.1250, 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, A:T.1479 Salt bridges: A:K.1280, A:R.1476, A:R.1476 ADP.7: 16 residues within 4Å: Chain B: I.1246, V.1247, I.1248, 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 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:I.1248, B:I.1248, B:P.1275, B:G.1277, B:S.1278, B:G.1279, B:K.1280, B:T.1281, B:M.1282, B:Y.1427, B:T.1479 Salt bridges: B:K.1280, B:R.1476, B:R.1476

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: T.937, D.1011, E.1051, E.1367, R.1408 Ligands: ATP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.937, A:E.1051 MG.8: 6 residues within 4Å: Chain B: T.937, D.1011, E.1051, E.1367, R.1405 Ligands: ATP.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.937, B:E.1051

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

SO4.4: 8 residues within 4Å: Chain A: S.1618, R.1619, T.1620, G.1621, K.1622, T.1623, I.1624, R.2115 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.1619, A:G.1621, A:K.1622, A:T.1623, A:T.1623, A:I.1624 Salt bridges: A:K.1622, A:R.2115 SO4.5: 8 residues within 4Å: Chain A: P.653, A.654, G.655, T.656, G.657, K.658, T.659, N.755 8 PLIP interactions: 8 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:N.755 Salt bridges: A:K.658 SO4.9: 6 residues within 4Å: Chain B: R.1619, G.1621, K.1622, T.1623, I.1624, R.2115 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:R.1619, B:G.1621, B:K.1622, B:T.1623, B:T.1623, B:T.1623, B:I.1624 Salt bridges: B:K.1622, B:R.2115 SO4.10: 7 residues within 4Å: Chain B: P.653, A.654, G.655, T.656, G.657, K.658, T.659 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:P.653, B:G.655, B:T.656, B:T.656, B:G.657, B:K.658, B:T.659, B:T.659 Salt bridges: B:K.658

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

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