SMTL ID : 3l43.2 (1 other biounit)

Crystal structure of the dynamin 3 GTPase domain bound with GDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

homo-dimer

Ligands

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

GDP.1: 17 residues within 4Å: Chain A: S.54, A.55, G.56, K.57, S.58, S.59, R.72, K.219, D.221, L.222, V.248, N.249, R.250, S.251, Q.252, I.255 Chain B: D.224 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.54, A:A.55, A:G.56, A:K.57, A:S.58, A:S.59, A:K.219, A:K.219, A:N.249, A:N.249 Water bridges: A:K.57, A:K.57 Salt bridges: A:K.57, A:R.72, A:D.221, B:D.224 GDP.3: 18 residues within 4Å: Chain A: D.224 Chain B: S.54, A.55, G.56, K.57, S.58, S.59, R.72, K.219, D.221, L.222, V.248, N.249, R.250, S.251, Q.252, I.255 Ligands: UNX.4 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.54, B:A.55, B:G.56, B:K.57, B:S.58, B:S.59, B:K.219, B:K.219, B:N.249, B:N.249, B:Q.252 Water bridges: B:K.57 Salt bridges: B:K.57, B:R.72, B:D.221, A:D.224

2 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.2: 5 residues within 4Å: Chain A: Q.53, V.77, T.78, P.151, G.152 No protein-ligand interaction detected (PLIP) UNX.4: 4 residues within 4Å: Chain B: S.58, T.78, D.149 Ligands: GDP.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, S. et al., Crystal structure of the dynamin 3 GTPase domain bound with GDP. to be published

Release Date

2010-01-19

Peptides

Dynamin-3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

Dynamin-3

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