SMTL ID : 2w6d.1

BACTERIAL DYNAMIN-LIKE PROTEIN LIPID TUBE BOUND

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 9.00 Å

Oligo State

homo-dimer

Ligands

44 x CPL: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-functional Binders)(Non-covalent)(Covalent)

CPL.1: 4 residues within 4Å: Ligands: CPL.3, CPL.15, CPL.19, CPL.22 No protein-ligand interaction detected (PLIP) CPL.3: 8 residues within 4Å: Chain A: A.586 Ligands: CPL.1, CPL.5, CPL.6, CPL.11, CPL.16, CPL.18, CPL.19 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.586 CPL.4: 6 residues within 4Å: Chain A: V.581, G.582, F.583 Ligands: CPL.5, CPL.6, CPL.13 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.583 CPL.5: 6 residues within 4Å: Chain A: G.582, L.584, Q.585, A.586 Ligands: CPL.3, CPL.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.585 CPL.6: 4 residues within 4Å: Ligands: CPL.3, CPL.4, CPL.16, CPL.19 No protein-ligand interaction detected (PLIP) CPL.7: 14 residues within 4Å: Chain A: T.414, F.415, E.416, N.417, D.418, F.419, L.420, D.587 Chain B: N.417, L.420, R.421, Q.423 Ligands: CPL.18, CPL.32 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:E.416, A:E.416, B:L.420 Hydrogen bonds: A:E.416, A:D.418, A:F.419, B:N.417 Salt bridges: A:D.418, B:R.421 CPL.8: 9 residues within 4Å: Chain A: F.429, L.432, S.433, S.434 Ligands: CPL.12, CPL.14, CPL.15, CPL.22, CPL.23 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.429, A:F.429 CPL.9: 9 residues within 4Å: Chain A: N.410, G.412, N.413, T.414, E.416, D.587, V.594 Ligands: CPL.10, CPL.21 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.594 CPL.10: 6 residues within 4Å: Chain B: E.425, K.446, E.449 Ligands: CPL.9, CPL.20, CPL.37 No protein-ligand interaction detected (PLIP) CPL.11: 20 residues within 4Å: Chain A: F.415, F.419, L.444, Q.445, F.448, I.452, I.557, G.558, G.559, I.560, I.561, T.562, V.564, T.565, L.568, I.572, L.576, L.579, R.590 Ligands: CPL.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.419, A:L.568, A:I.572, A:I.572, A:L.576, A:L.579, A:R.590 Hydrogen bonds: A:T.565 CPL.12: 3 residues within 4Å: Chain A: F.429 Ligands: CPL.8, CPL.17 No protein-ligand interaction detected (PLIP) CPL.13: 7 residues within 4Å: Chain A: L.577, G.578, V.581, G.582, F.583 Ligands: CPL.4, CPL.16 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.577, A:L.577, A:V.581, A:F.583, A:F.583, A:F.583, A:F.583 CPL.14: 10 residues within 4Å: Chain A: E.425, L.426, N.427, K.446, A.447, E.449, Q.450 Ligands: CPL.8, CPL.22, CPL.36 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.425 Hydrogen bonds: A:E.425, A:E.425 Salt bridges: A:E.449 CPL.15: 9 residues within 4Å: Chain A: L.432, S.433, S.434, G.435, K.436 Ligands: CPL.1, CPL.8, CPL.16, CPL.19 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.432, A:L.432 CPL.16: 8 residues within 4Å: Chain A: L.576, L.579, G.580, V.581 Ligands: CPL.3, CPL.6, CPL.13, CPL.15 No protein-ligand interaction detected (PLIP) CPL.17: 3 residues within 4Å: Ligands: CPL.12, CPL.22, CPL.25 No protein-ligand interaction detected (PLIP) CPL.18: 3 residues within 4Å: Ligands: CPL.3, CPL.7, CPL.26 No protein-ligand interaction detected (PLIP) CPL.19: 5 residues within 4Å: Ligands: CPL.1, CPL.3, CPL.6, CPL.15, CPL.23 No protein-ligand interaction detected (PLIP) CPL.20: 4 residues within 4Å: Ligands: CPL.10, CPL.21, CPL.40, CPL.43 No protein-ligand interaction detected (PLIP) CPL.21: 2 residues within 4Å: Ligands: CPL.9, CPL.20 No protein-ligand interaction detected (PLIP) CPL.22: 7 residues within 4Å: Ligands: CPL.1, CPL.8, CPL.14, CPL.17, CPL.23, CPL.24, CPL.25 No protein-ligand interaction detected (PLIP) CPL.23: 3 residues within 4Å: Ligands: CPL.8, CPL.19, CPL.22 No protein-ligand interaction detected (PLIP) CPL.24: 3 residues within 4Å: Ligands: CPL.22, CPL.26, CPL.36 No protein-ligand interaction detected (PLIP) CPL.25: 3 residues within 4Å: Ligands: CPL.17, CPL.22, CPL.27 No protein-ligand interaction detected (PLIP) CPL.26: 3 residues within 4Å: Ligands: CPL.18, CPL.24, CPL.32 No protein-ligand interaction detected (PLIP) CPL.27: 1 residues within 4Å: Ligands: CPL.25 No protein-ligand interaction detected (PLIP) CPL.28: 6 residues within 4Å: Chain B: V.581, G.582, Q.585 Ligands: CPL.31, CPL.41, CPL.46 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Q.585, B:Q.585 CPL.29: 20 residues within 4Å: Chain B: N.441, L.444, I.561, T.562, V.564, T.565, G.566, L.568, L.569, I.572, G.573, L.576, L.579, A.586, D.587, R.590, L.593 Ligands: CPL.30, CPL.36, CPL.46 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.572, B:I.572, B:L.576, B:L.576, B:L.579, B:A.586, B:R.590, B:L.593 Hydrogen bonds: B:L.568 CPL.30: 6 residues within 4Å: Chain B: K.436, G.580 Ligands: CPL.29, CPL.31, CPL.33, CPL.46 No protein-ligand interaction detected (PLIP) CPL.31: 6 residues within 4Å: Chain B: L.577, G.580, V.581 Ligands: CPL.28, CPL.30, CPL.41 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.577, B:V.581, B:V.581 CPL.32: 15 residues within 4Å: Chain A: N.417, L.420, R.421, Q.423 Chain B: T.414, F.415, E.416, N.417, D.418, F.419, L.420, R.421 Ligands: CPL.7, CPL.26, CPL.36 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:E.416, A:L.420 Hydrogen bonds: B:N.417, B:L.420, B:R.421, A:N.417, A:R.421, A:R.421 Salt bridges: B:D.418 CPL.33: 7 residues within 4Å: Chain B: L.432, S.433, S.434, G.435 Ligands: CPL.30, CPL.42, CPL.44 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.432, B:L.432 CPL.34: 3 residues within 4Å: Chain B: F.429 Ligands: CPL.39, CPL.45 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.429, B:F.429 CPL.35: 13 residues within 4Å: Chain B: N.413, A.586, D.587, Q.588, R.590, R.591, E.592, V.594, K.595, K.598, K.599, V.602 Ligands: CPL.36 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:D.587, B:R.591, B:R.591, B:V.594, B:V.594, B:K.595, B:K.598 Salt bridges: B:K.598, B:K.598, B:K.598 CPL.36: 14 residues within 4Å: Chain B: N.410, G.412, N.413, T.414, F.415, E.416, N.417, D.587, R.590 Ligands: CPL.14, CPL.24, CPL.29, CPL.32, CPL.35 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:D.587, B:R.590, B:R.590 Hydrogen bonds: B:E.416 CPL.37: 11 residues within 4Å: Chain B: P.424, E.425, L.426, N.427, L.428, A.443, K.446, A.447, E.449 Ligands: CPL.10, CPL.43 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:E.425, B:L.428, B:L.428 Hydrogen bonds: B:E.425, B:E.425, B:L.426, B:N.427 Salt bridges: B:E.449 CPL.39: 4 residues within 4Å: Ligands: CPL.34, CPL.40, CPL.42, CPL.43 No protein-ligand interaction detected (PLIP) CPL.40: 3 residues within 4Å: Ligands: CPL.20, CPL.39, CPL.45 No protein-ligand interaction detected (PLIP) CPL.41: 2 residues within 4Å: Ligands: CPL.28, CPL.31 No protein-ligand interaction detected (PLIP) CPL.42: 3 residues within 4Å: Ligands: CPL.33, CPL.39, CPL.44 No protein-ligand interaction detected (PLIP) CPL.43: 3 residues within 4Å: Ligands: CPL.20, CPL.37, CPL.39 No protein-ligand interaction detected (PLIP) CPL.44: 3 residues within 4Å: Ligands: CPL.33, CPL.42, CPL.46 No protein-ligand interaction detected (PLIP) CPL.45: 2 residues within 4Å: Ligands: CPL.34, CPL.40 No protein-ligand interaction detected (PLIP) CPL.46: 4 residues within 4Å: Ligands: CPL.28, CPL.29, CPL.30, CPL.44 No protein-ligand interaction detected (PLIP)

2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Covalent)

GDP.2: 23 residues within 4Å: Chain A: D.77, K.79, R.80, G.81, K.82, S.83, T.84, S.97, R.209, N.238, A.239, D.241, Q.242, S.291, S.292, I.293 Chain B: Q.242, V.243, R.244, E.245, S.246, L.247, S.259 19 PLIP interactions: 4 interactions with chain B, 15 interactions with chain A Hydrogen bonds: B:E.245, B:S.259, B:S.259, A:K.79, A:R.80, A:G.81, A:S.83, A:T.84, A:R.209, A:N.238, A:A.239, A:Q.242, A:S.292, A:I.293 Salt bridges: B:E.245, A:K.79, A:K.82, A:D.241 pi-Cation interactions: A:R.209 GDP.38: 23 residues within 4Å: Chain A: Q.242, V.243, R.244, E.245, S.246, L.247, S.259 Chain B: D.77, K.79, R.80, G.81, K.82, S.83, T.84, S.97, R.209, N.238, A.239, D.241, Q.242, S.291, S.292, I.293 21 PLIP interactions: 17 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:K.79, B:R.80, B:G.81, B:S.83, B:T.84, B:T.84, B:R.209, B:R.209, B:N.238, B:A.239, B:Q.242, B:S.292, B:I.293, A:E.245, A:S.259, A:S.259 Salt bridges: B:K.79, B:K.82, B:D.241, A:E.245 pi-Cation interactions: B:R.209

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Low, H.H. et al., Structure of a Bacterial Dynamin-Like Protein Lipid Tube Provides a Mechanism for Assembly and Membrane Curving. Cell(Cambridge,Mass.) (2009)

Release Date

2009-12-22

Peptides

DYNAMIN FAMILY PROTEIN: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DYNAMIN FAMILY PROTEIN

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