SMTL ID : 1g16.1

CRYSTAL STRUCTURE OF SEC4-GDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

8 x CO: COBALT (II) ION(Non-covalent)

CO.1: 2 residues within 4Å: Chain A: S.17 Ligands: GDP.3 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.17, H2O.1, H2O.1, H2O.1, H2O.1 CO.2: 2 residues within 4Å: Chain A: D.26, D.149 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.26, A:D.26, A:D.149, H2O.1, H2O.1 CO.4: 3 residues within 4Å: Chain B: S.17, D.58 Ligands: GDP.5 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.17, H2O.5, H2O.5, H2O.5, H2O.5 CO.6: 4 residues within 4Å: Chain C: S.17, D.58, T.59 Ligands: GDP.8 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:S.17, H2O.8, H2O.8, H2O.8, H2O.8 CO.7: 3 residues within 4Å: Chain C: D.26, D.149, N.153 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.149, H2O.8, H2O.8, H2O.8, H2O.8 CO.9: 3 residues within 4Å: Chain D: S.17, D.58 Ligands: GDP.12 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:S.17, H2O.11, H2O.11, H2O.11, H2O.11 CO.10: 3 residues within 4Å: Chain D: D.26, D.149, N.153 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.26, D:D.149, H2O.11, H2O.11, H2O.11 CO.11: 1 residues within 4Å: Chain D: H.104 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.104, H2O.11, H2O.11

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

GDP.3: 20 residues within 4Å: Chain A: D.11, S.12, G.13, V.14, G.15, K.16, S.17, C.18, F.28, N.29, P.30, E.63, N.116, K.117, D.119, M.120, S.145, A.146, K.147 Ligands: CO.1 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:G.13, A:V.14, A:G.15, A:K.16, A:S.17, A:C.18, A:N.29, A:E.63, A:N.116, A:K.117, A:K.117, A:A.146, A:K.147 Water bridges: A:S.17, A:T.59, A:R.64, A:R.64 Salt bridges: A:K.16, A:D.119 pi-Stacking: A:F.28, A:F.28 GDP.5: 18 residues within 4Å: Chain B: D.11, S.12, G.13, V.14, G.15, K.16, S.17, C.18, F.28, P.30, N.116, K.117, D.119, M.120, S.145, A.146, K.147 Ligands: CO.4 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:G.13, B:V.14, B:G.15, B:K.16, B:S.17, B:C.18, B:E.63, B:N.116, B:K.117, B:K.117, B:A.146, B:K.147 Water bridges: B:K.16, B:R.64 Salt bridges: B:K.16, B:D.119 pi-Stacking: B:F.28, B:F.28 GDP.8: 19 residues within 4Å: Chain C: D.11, S.12, G.13, V.14, G.15, K.16, S.17, C.18, F.28, N.29, P.30, N.116, K.117, D.119, M.120, S.145, A.146, K.147 Ligands: CO.6 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:S.12, C:G.13, C:V.14, C:G.15, C:K.16, C:S.17, C:C.18, C:N.29, C:N.116, C:K.117, C:K.117, C:A.146, C:K.147 Water bridges: C:K.16, C:S.17, C:K.117 Salt bridges: C:K.16, C:D.119 pi-Stacking: C:F.28, C:F.28 GDP.12: 18 residues within 4Å: Chain D: D.11, S.12, G.13, V.14, G.15, K.16, S.17, C.18, F.28, P.30, N.116, K.117, D.119, M.120, S.145, A.146, K.147 Ligands: CO.9 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:G.13, D:V.14, D:G.15, D:K.16, D:S.17, D:C.18, D:N.116, D:K.117, D:K.117, D:A.146, D:K.147 Water bridges: D:G.10, D:K.16, D:S.17 Salt bridges: D:K.16, D:D.119 pi-Stacking: D:F.28, D:F.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stroupe, C. et al., Crystal structures of a Rab protein in its inactive and active conformations. J.Mol.Biol. (2000)

Release Date

2000-12-11

Peptides

RAS-RELATED PROTEIN SEC4: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

RAS-RELATED PROTEIN SEC4

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