SMTL ID : 1d2n.1

D2 DOMAIN OF N-ETHYLMALEIMIDE-SENSITIVE FUSION PROTEIN

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-hexamer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: T.78 Ligands: ANP.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.78, H2O.6, H2O.6, H2O.6 MG.4: 2 residues within 4Å: Chain B: T.78 Ligands: ANP.5 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.78, H2O.16, H2O.16, H2O.16 MG.7: 2 residues within 4Å: Chain C: T.78 Ligands: ANP.8 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.78, H2O.27, H2O.27, H2O.27 MG.10: 2 residues within 4Å: Chain D: T.78 Ligands: ANP.11 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:T.78, H2O.37, H2O.37, H2O.37 MG.13: 2 residues within 4Å: Chain E: T.78 Ligands: ANP.14 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:T.78, H2O.48, H2O.48, H2O.48 MG.16: 2 residues within 4Å: Chain F: T.78 Ligands: ANP.17 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:T.78, H2O.58, H2O.58, H2O.58

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

ANP.2: 22 residues within 4Å: Chain A: I.31, M.32, N.33, G.34, I.35, I.36, W.38, V.42, P.73, H.74, S.75, G.76, K.77, T.78, A.79, L.80, S.175, I.235, K.236, L.239 Chain F: K.159 Ligands: MG.1 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain F Hydrogen bonds: A:I.31, A:M.32, A:N.33, A:N.33, A:I.36, A:I.36, A:H.74, A:G.76, A:K.77, A:K.77, A:K.77, A:T.78, A:A.79, A:S.175, F:K.159, F:K.159 Salt bridges: A:K.236 ANP.5: 22 residues within 4Å: Chain B: I.31, M.32, N.33, G.34, I.35, I.36, W.38, V.42, P.73, H.74, S.75, G.76, K.77, T.78, A.79, L.80, S.175, I.235, K.236, L.239 Chain D: K.159 Ligands: MG.4 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:I.31, B:M.32, B:N.33, B:N.33, B:I.36, B:I.36, B:H.74, B:G.76, B:K.77, B:K.77, B:K.77, B:T.78, B:A.79, B:S.175, D:K.159, D:K.159 Salt bridges: B:K.236 ANP.8: 22 residues within 4Å: Chain C: I.31, M.32, N.33, G.34, I.35, I.36, W.38, V.42, P.73, H.74, S.75, G.76, K.77, T.78, A.79, L.80, S.175, I.235, K.236, L.239 Chain E: K.159 Ligands: MG.7 17 PLIP interactions: 15 interactions with chain C, 2 interactions with chain E Hydrogen bonds: C:I.31, C:M.32, C:N.33, C:N.33, C:I.36, C:I.36, C:H.74, C:G.76, C:K.77, C:K.77, C:K.77, C:T.78, C:A.79, C:S.175, E:K.159, E:K.159 Salt bridges: C:K.236 ANP.11: 22 residues within 4Å: Chain C: K.159 Chain D: I.31, M.32, N.33, G.34, I.35, I.36, W.38, V.42, P.73, H.74, S.75, G.76, K.77, T.78, A.79, L.80, S.175, I.235, K.236, L.239 Ligands: MG.10 17 PLIP interactions: 15 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:I.31, D:M.32, D:N.33, D:N.33, D:I.36, D:I.36, D:H.74, D:G.76, D:K.77, D:K.77, D:K.77, D:T.78, D:A.79, D:S.175, C:K.159, C:K.159 Salt bridges: D:K.236 ANP.14: 22 residues within 4Å: Chain A: K.159 Chain E: I.31, M.32, N.33, G.34, I.35, I.36, W.38, V.42, P.73, H.74, S.75, G.76, K.77, T.78, A.79, L.80, S.175, I.235, K.236, L.239 Ligands: MG.13 17 PLIP interactions: 15 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:I.31, E:M.32, E:N.33, E:N.33, E:I.36, E:I.36, E:H.74, E:G.76, E:K.77, E:K.77, E:K.77, E:T.78, E:A.79, E:S.175, A:K.159, A:K.159 Salt bridges: E:K.236 ANP.17: 22 residues within 4Å: Chain B: K.159 Chain F: I.31, M.32, N.33, G.34, I.35, I.36, W.38, V.42, P.73, H.74, S.75, G.76, K.77, T.78, A.79, L.80, S.175, I.235, K.236, L.239 Ligands: MG.16 17 PLIP interactions: 15 interactions with chain F, 2 interactions with chain B Hydrogen bonds: F:I.31, F:M.32, F:N.33, F:N.33, F:I.36, F:I.36, F:H.74, F:G.76, F:K.77, F:K.77, F:K.77, F:T.78, F:A.79, F:S.175, B:K.159, B:K.159 Salt bridges: F:K.236

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: D.216, K.217, T.220 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.217, A:T.221 GOL.6: 3 residues within 4Å: Chain B: D.216, K.217, T.220 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.217, B:T.221 GOL.9: 3 residues within 4Å: Chain C: D.216, K.217, T.220 2 PLIP interactions: 2 interactions with chain C Water bridges: C:K.217, C:T.221 GOL.12: 3 residues within 4Å: Chain D: D.216, K.217, T.220 2 PLIP interactions: 2 interactions with chain D Water bridges: D:K.217, D:T.221 GOL.15: 3 residues within 4Å: Chain E: D.216, K.217, T.220 2 PLIP interactions: 2 interactions with chain E Water bridges: E:K.217, E:T.221 GOL.18: 3 residues within 4Å: Chain F: D.216, K.217, T.220 2 PLIP interactions: 2 interactions with chain F Water bridges: F:K.217, F:T.221

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lenzen, C.U. et al., Crystal structure of the hexamerization domain of N-ethylmaleimide-sensitive fusion protein. Cell(Cambridge,Mass.) (1998)

Release Date

1998-10-14

Peptides

N-ETHYLMALEIMIDE-SENSITIVE FUSION PROTEIN: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

N-ETHYLMALEIMIDE-SENSITIVE FUSION PROTEIN