SMTL ID : 6ekk.2 (1 other biounit)

Crystal structure of GEF domain of DENND 1A in complex with Rab GTPase Rab35-GDP bound state.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

hetero-1-1-mer

Ligands

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: Q.68, N.69, N.113 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.69, A:N.113, A:N.113 Water bridges: A:Q.68, A:Q.68, A:N.69, A:R.169, A:R.169 SO4.2: 4 residues within 4Å: Chain A: K.5, Q.6, N.7, K.80 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.4, A:Q.6, A:N.7 Salt bridges: A:K.5, A:K.80 SO4.3: 5 residues within 4Å: Chain A: E.44, V.45, T.48 Chain B: T.37, T.38 3 PLIP interactions: 3 interactions with chain B Water bridges: B:T.37, B:T.38, B:T.38 SO4.8: 5 residues within 4Å: Chain B: C.112, R.113, G.141, I.142, L.165 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.111, B:R.113 Water bridges: B:R.113 Salt bridges: B:R.113 SO4.9: 6 residues within 4Å: Chain A: I.77 Chain B: S.20, S.34, I.36, T.37 Ligands: GDP.10 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.20, B:S.34 Water bridges: B:S.20, B:S.34, B:I.36, B:T.37, B:T.37

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 6 residues within 4Å: Chain A: R.3, Q.81, A.214, Y.221, W.222, Y.226 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.3, A:Q.81, A:A.214, A:W.222 EDO.5: 1 residues within 4Å: Chain A: R.122 No protein-ligand interaction detected (PLIP) EDO.6: 9 residues within 4Å: Chain A: N.69, F.70, Y.109, R.169, N.170, E.173, S.204, T.207, A.208 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.69, A:A.208 Water bridges: A:T.71, A:T.71 EDO.7: 6 residues within 4Å: Chain A: F.336, E.338, T.358, F.363, K.364, I.367 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.338, A:K.364

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

GDP.10: 15 residues within 4Å: Chain B: D.14, S.15, G.16, V.17, G.18, K.19, S.20, S.21, N.118, K.119, D.121, S.148, A.149, K.150 Ligands: SO4.9 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:D.14, B:G.16, B:V.17, B:G.18, B:K.19, B:S.20, B:S.20, B:S.21, B:S.21, B:N.118, B:K.119, B:K.119, B:A.149, B:K.150 Water bridges: B:S.15, B:K.19, B:S.20, B:S.20, B:K.119, B:D.121, B:K.150 Salt bridges: B:D.121

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Srikannathasan, V., Crystal structure of DENND1A-RAB35 complex with GDP bound state. To be published

Release Date

2018-10-17

Peptides

DENN domain-containing protein 1A: A
Ras-related protein Rab-35: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

DENN domain-containing protein 1A

Ras-related protein Rab-35

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