SMTL ID : 3vkg.1 (2 other biounits)

X-ray structure of an MTBD truncation mutant of dynein motor domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.81 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 14 residues within 4Å: Chain A: L.584, V.585, T.590, A.613, G.614, T.615, G.616, K.617, T.618, E.619, I.745, L.786, R.787, K.790 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:V.585, A:V.585, A:G.614, A:T.615, A:T.615, A:G.616, A:K.617, A:T.618, A:T.618, A:E.619, A:E.619, A:R.787, A:R.787, A:K.790 Salt bridges: A:K.617 ADP.2: 16 residues within 4Å: Chain A: L.886, V.887, W.892, G.916, G.917, G.918, K.919, T.920, T.921, E.1033, L.1058, M.1062, N.1066, R.1443, R.1446 Ligands: MG.7 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:V.887, A:W.892, A:G.916, A:G.917, A:G.918, A:G.918, A:K.919, A:T.920, A:T.921, A:T.921, A:N.1066, A:R.1446 Salt bridges: A:K.919, A:R.1443, A:R.1446, A:R.1446 ADP.3: 17 residues within 4Å: Chain A: V.1283, V.1284, I.1285, T.1287, T.1290, P.1313, G.1314, S.1315, G.1316, K.1317, T.1318, M.1319, I.1464, Y.1465, P.1513, R.1514, S.1517 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:I.1285, A:I.1285, A:G.1314, A:S.1315, A:G.1316, A:K.1317, A:T.1318, A:M.1319, A:S.1517 Salt bridges: A:K.1317 ADP.4: 14 residues within 4Å: Chain A: P.1624, L.1625, V.1626, F.1628, V.1631, S.1655, G.1656, G.1657, G.1658, K.1659, S.1660, V.1661, W.1813, F.1825 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:V.1626, A:V.1626, A:G.1656, A:G.1657, A:G.1658, A:K.1659, A:S.1660, A:V.1661, A:R.1664 Salt bridges: A:K.1659 pi-Stacking: A:W.1813, A:W.1813 ADP.8: 15 residues within 4Å: Chain B: L.584, V.585, T.590, A.613, G.614, T.615, G.616, K.617, T.618, E.619, I.745, L.786, R.787, K.790 Ligands: MG.14 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:V.585, B:V.585, B:G.614, B:T.615, B:G.616, B:G.616, B:K.617, B:T.618, B:E.619, B:E.619, B:E.619, B:R.787, B:R.787 Salt bridges: B:K.617 ADP.9: 15 residues within 4Å: Chain B: L.886, V.887, W.892, G.916, G.917, G.918, K.919, T.920, T.921, E.1033, L.1058, M.1062, N.1066, R.1446 Ligands: MG.15 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:V.887, B:W.892, B:G.916, B:G.917, B:G.918, B:G.918, B:K.919, B:T.920, B:T.921, B:N.1066, B:R.1446 Salt bridges: B:K.919, B:R.1446, B:R.1446 pi-Stacking: B:W.892 ADP.10: 17 residues within 4Å: Chain B: V.1283, V.1284, I.1285, T.1290, P.1313, G.1314, S.1315, G.1316, K.1317, T.1318, M.1319, I.1464, Y.1465, F.1468, P.1513, R.1514, S.1517 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:I.1285, B:I.1285, B:G.1314, B:S.1315, B:G.1316, B:G.1316, B:K.1317, B:T.1318, B:M.1319, B:Y.1465, B:S.1517 Salt bridges: B:K.1317, B:R.1514, B:R.1514 ADP.11: 16 residues within 4Å: Chain B: V.1623, P.1624, L.1625, V.1626, F.1628, V.1631, S.1655, G.1656, G.1657, G.1658, K.1659, S.1660, V.1661, W.1813, R.1895, L.1898 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:V.1626, B:V.1626, B:V.1654, B:G.1656, B:G.1657, B:G.1658, B:G.1658, B:K.1659, B:S.1660, B:V.1661 Salt bridges: B:K.1659, B:R.1895, B:R.1895 pi-Stacking: B:W.1813

4 x SPM: SPERMINE(Non-covalent)

SPM.5: 3 residues within 4Å: Chain A: F.1076, E.1303, H.1304 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:H.1304 Hydrogen bonds: A:H.1304 SPM.6: 7 residues within 4Å: Chain A: A.2603, F.2604, H.2605, S.2606, S.2931, S.2935, R.2939 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.2602, A:S.2606, A:S.2935, A:S.2935 SPM.12: 8 residues within 4Å: Chain B: Y.1067, L.1071, E.1074, P.1075, F.1076, N.1179, E.1303, R.1305 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.1076 Hydrogen bonds: B:E.1303 SPM.13: 8 residues within 4Å: Chain B: K.2602, A.2603, F.2604, H.2605, S.2606, S.2931, S.2935, L.3175 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.2602, B:S.2606, B:S.2606

3 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 6 residues within 4Å: Chain A: T.920, E.1033, E.1405, R.1443, R.1446 Ligands: ADP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.920, A:E.1033 MG.14: 3 residues within 4Å: Chain B: T.618, D.663 Ligands: ADP.8 No protein-ligand interaction detected (PLIP) MG.15: 4 residues within 4Å: Chain B: T.920, E.1033, E.1405 Ligands: ADP.9 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.920, B:E.1033

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kon, T. et al., The 2.8 A crystal structure of the dynein motor domain. Nature (2012)

Release Date

2012-03-14

Peptides

Dynein heavy chain, cytoplasmic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dynein heavy chain, cytoplasmic

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