SMTL ID : 4w8f.3 (2 other biounits)

Crystal structure of the dynein motor domain in the AMPPNP-bound state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.54 Å

Oligo State

homo-dimer

Ligands

8 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 19 residues within 4Å: Chain A: L.407, I.408, T.410, L.413, P.435, A.436, G.437, T.438, G.439, K.440, T.441, E.442, Q.487, N.537, I.567, I.571, L.608, R.609, K.612 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:I.408, A:I.408, A:G.437, A:T.438, A:K.440, A:T.441, A:T.441, A:T.441, A:E.442, A:N.537, A:R.609, A:K.612 ANP.2: 26 residues within 4Å: Chain A: F.685, S.686, F.691, K.713, A.714, G.715, C.716, G.717, K.718, T.719, A.720, E.833, V.857, C.858, S.862, K.863, H.866, L.867, F.919, E.923, R.1145, E.1149, R.1187, R.1190, H.1191 Ligands: MG.5 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:S.686, A:S.686, A:G.715, A:C.716, A:G.717, A:K.718, A:K.718, A:T.719, A:T.719, A:A.720, A:E.833, A:K.863, A:H.866, A:E.923, A:R.1145, A:R.1145, A:R.1187, A:R.1187, A:R.1190, A:R.1190 Salt bridges: A:R.1190 pi-Stacking: A:F.685, A:F.685 ANP.3: 26 residues within 4Å: Chain A: I.1028, V.1029, I.1030, T.1032, T.1035, P.1057, P.1058, G.1059, S.1060, G.1061, K.1062, T.1063, M.1064, E.1126, N.1174, P.1200, I.1208, Y.1209, Y.1212, P.1257, R.1258, T.1261, A.1474, P.1544, A.1545, R.1549 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:I.1030, A:I.1030, A:P.1057, A:G.1059, A:G.1061, A:K.1062, A:K.1062, A:T.1063, A:T.1063, A:T.1063, A:M.1064, A:E.1126, A:E.1126, A:N.1174, A:N.1174, A:R.1258, A:R.1258, A:T.1261, A:T.1261, A:R.1549 Salt bridges: A:R.1258 ANP.4: 22 residues within 4Å: Chain A: V.1368, P.1369, M.1370, V.1371, H.1373, S.1400, R.1401, T.1402, G.1403, K.1404, T.1405, I.1406, D.1456, T.1528, C.1530, W.1558, V.1566, M.1570, I.1631, R.1635, F.2065, R.2069 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:V.1371, A:V.1371, A:H.1373, A:S.1400, A:R.1401, A:R.1401, A:R.1401, A:T.1402, A:G.1403, A:K.1404, A:K.1404, A:T.1405, A:T.1405, A:I.1406, A:D.1456, A:D.1456, A:T.1528, A:R.1635, A:R.2069, A:R.2069, A:R.2069 Salt bridges: A:R.2069 ANP.6: 20 residues within 4Å: Chain B: L.407, I.408, T.410, L.413, A.436, G.437, T.438, G.439, K.440, T.441, E.442, D.486, Q.487, T.535, N.537, I.567, I.571, L.608, R.609, K.612 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:I.408, B:I.408, B:G.437, B:G.439, B:K.440, B:K.440, B:T.441, B:T.441, B:T.441, B:T.441, B:E.442, B:N.537, B:R.609, B:R.609, B:K.612 ANP.7: 27 residues within 4Å: Chain B: F.685, S.686, M.687, F.691, K.713, A.714, G.715, C.716, G.717, K.718, T.719, A.720, E.833, V.857, C.858, S.862, K.863, H.866, L.867, F.919, E.923, R.1145, E.1149, R.1187, R.1190, H.1191 Ligands: MG.10 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:S.686, B:S.686, B:G.715, B:C.716, B:G.717, B:K.718, B:K.718, B:T.719, B:T.719, B:T.719, B:A.720, B:K.863, B:H.866, B:R.1145, B:R.1145, B:R.1187, B:R.1187, B:R.1190, B:R.1190 Salt bridges: B:R.1190 ANP.8: 25 residues within 4Å: Chain B: I.1028, V.1029, I.1030, T.1032, T.1035, P.1057, P.1058, G.1059, S.1060, G.1061, K.1062, T.1063, M.1064, E.1126, N.1174, P.1200, I.1208, Y.1209, Y.1212, P.1257, R.1258, T.1261, P.1544, A.1545, R.1549 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:I.1030, B:I.1030, B:G.1059, B:S.1060, B:S.1060, B:G.1061, B:K.1062, B:K.1062, B:T.1063, B:T.1063, B:T.1063, B:M.1064, B:E.1126, B:Y.1209, B:R.1258, B:R.1258, B:T.1261, B:T.1261, B:R.1549, B:R.1549 Salt bridges: B:R.1258 ANP.9: 23 residues within 4Å: Chain B: V.1368, P.1369, M.1370, V.1371, H.1373, M.1376, S.1400, R.1401, T.1402, G.1403, K.1404, T.1405, I.1406, D.1456, C.1530, W.1558, V.1566, M.1570, I.1631, R.1635, R.2025, F.2065, R.2069 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:V.1371, B:V.1371, B:H.1373, B:R.1401, B:R.1401, B:R.1401, B:T.1402, B:G.1403, B:K.1404, B:K.1404, B:T.1405, B:T.1405, B:I.1406, B:D.1456, B:R.1635, B:R.2025, B:R.2069, B:R.2069 Salt bridges: B:R.2069

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 8 residues within 4Å: Chain A: T.719, D.793, E.833, R.1145, E.1149, R.1187, R.1190 Ligands: ANP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.719, A:E.833 MG.10: 7 residues within 4Å: Chain B: T.719, D.793, E.833, R.1145, E.1149, R.1187 Ligands: ANP.7 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.719, B:E.833

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bhabha, G. et al., Allosteric communication in the Dynein motor domain. Cell (2014)

Release Date

2014-11-12

Peptides

Dynein heavy chain lysozyme chimera: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dynein heavy chain lysozyme chimera

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