SMTL ID : 3w6p.1

Crystal structure of human Dlp1 in complex with GDP.AlF4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 22 residues within 4Å: Chain A: S.37, S.38, G.39, K.40, S.41, S.42, R.55, G.56, T.57, K.218, D.220, L.221, V.247, N.248, R.249, S.250, Q.251, I.254 Chain B: D.223 Ligands: ALF.2, MG.3, NA.4 23 PLIP interactions: 21 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.37, A:S.38, A:G.39, A:K.40, A:S.41, A:S.42, A:S.42, A:G.56, A:T.61, A:K.218, A:K.218, A:N.248, A:Q.251 Water bridges: A:T.61, A:T.61, A:G.151, A:D.220, A:S.250, B:D.223 Salt bridges: A:K.40, A:D.220, B:D.223 pi-Cation interactions: A:K.218 GDP.5: 22 residues within 4Å: Chain A: D.223 Chain B: S.37, S.38, G.39, K.40, S.41, S.42, R.55, G.56, T.57, K.218, D.220, L.221, V.247, N.248, R.249, S.250, Q.251, I.254 Ligands: ALF.6, MG.7, NA.8 25 PLIP interactions: 23 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.37, B:S.38, B:G.39, B:K.40, B:S.41, B:S.42, B:S.42, B:G.56, B:T.57, B:T.61, B:K.218, B:K.218, B:N.248, B:Q.251 Water bridges: B:T.61, B:T.61, B:G.151, B:D.220, B:N.248, B:S.250, A:D.223 Salt bridges: B:K.40, B:D.220, A:D.223 pi-Cation interactions: B:K.218

2 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.2: 12 residues within 4Å: Chain A: Q.36, S.37, K.40, G.58, I.59, V.60, T.61, L.149, G.151 Ligands: GDP.1, MG.3, NA.4 No protein-ligand interaction detected (PLIP) ALF.6: 12 residues within 4Å: Chain B: Q.36, S.37, K.40, G.58, I.59, V.60, T.61, L.149, G.151 Ligands: GDP.5, MG.7, NA.8 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: S.41, T.61 Ligands: GDP.1, ALF.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.41, A:T.61, H2O.8, H2O.8 MG.7: 4 residues within 4Å: Chain B: S.41, T.61 Ligands: GDP.5, ALF.6 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.41, B:T.61, H2O.22, H2O.22

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 7 residues within 4Å: Chain A: S.37, G.56, T.57, G.58, V.60 Ligands: GDP.1, ALF.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.37, A:S.37, A:V.60 NA.8: 6 residues within 4Å: Chain B: S.37, G.56, G.58, V.60 Ligands: GDP.5, ALF.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.37, B:G.58, B:V.60

1 x CA: CALCIUM ION(Non-functional Binders)

CA.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.10: 6 residues within 4Å: Chain A: L.221, M.222, A.224 Chain B: L.221, M.222, A.224 No protein-ligand interaction detected (PLIP) PG4.11: 3 residues within 4Å: Chain B: R.174, F.175, N.178 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kishida, H. et al., Crystal structure of GTPase domain fused with minimal stalks from human dynamin-1-like protein (Dlp1) in complex with several nucleotide analogues. CURR TOP PEPT PROTEIN RES. (2013)

Release Date

2014-02-19

Peptides

Dynamin-1-like protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dynamin-1-like protein

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