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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

hetero-1-1-mer

Ligands

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

SO4.1: 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:Q.6, A:N.7, A:N.7 Salt bridges: A:K.5, A:K.80 SO4.2: 5 residues within 4Å: Chain A: D.236, C.239 Chain B: F.43, I.45, Q.58 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.58 SO4.6: 4 residues within 4Å: Chain B: K.98, H.102, F.136, Q.139 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.98, B:H.102 SO4.7: 3 residues within 4Å: Chain B: N.29, T.30, F.31 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.29, B:T.30, B:F.31

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

EDO.3: 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:Q.81, A:A.214, A:W.222 Water bridges: A:Q.81 EDO.4: 7 residues within 4Å: Chain A: F.70, Y.109, R.169, N.170, E.173, S.204, T.207 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.170, A:A.208 Water bridges: A:T.71 EDO.5: 3 residues within 4Å: Chain A: F.105, N.170, H.211 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.170, A:H.211 Water bridges: A:N.168 EDO.8: 5 residues within 4Å: Chain B: F.31, G.33, S.34, Y.35, T.38 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:S.34, A:T.48 Hydrogen bonds: A:T.48

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

GDP.9: 14 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 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: 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:K.119, B:D.121 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
A

B
C

DENN domain-containing protein 1A

Ras-related protein Rab-35

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