SMTL ID : 3syn.5 (4 other biounits)

Crystal structure of FlhF in complex with its activator

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.06 Å

Oligo State

hetero-4-4-mer

Ligands

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

GDP.1: 22 residues within 4Å: Chain A: S.113, G.115, A.116, G.117, K.118, T.119, T.120, R.146, Q.152, K.248, D.250, E.251, T.273, N.274, G.275, Q.276 Chain B: T.114, R.146 Chain C: Q.8 Ligands: MG.2, AF3.3, AF3.11 22 PLIP interactions: 19 interactions with chain A, 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: A:G.115, A:G.117, A:K.118, A:T.119, A:T.120, A:T.120, A:T.120, A:R.146, A:Q.152, A:Q.152, A:K.248, A:K.248, A:T.273, A:G.275, B:T.114, C:Q.8 Water bridges: A:T.119, A:Q.276, B:R.146 Salt bridges: A:K.118, A:D.250, A:E.251 GDP.9: 23 residues within 4Å: Chain A: T.114, R.146 Chain B: S.113, G.115, A.116, G.117, K.118, T.119, T.120, R.146, Q.152, K.248, D.250, E.251, T.273, N.274, G.275, Q.276 Chain D: Q.8 Ligands: AF3.3, SO4.4, MG.10, AF3.11 24 PLIP interactions: 20 interactions with chain B, 2 interactions with chain A, 2 interactions with chain D Hydrogen bonds: B:G.115, B:A.116, B:G.117, B:K.118, B:T.119, B:T.119, B:T.120, B:T.120, B:R.146, B:Q.152, B:Q.152, B:K.248, B:K.248, B:T.273, B:G.275, A:T.114, D:Q.8, D:Q.8 Water bridges: B:T.119, B:Q.276, A:R.146 Salt bridges: B:K.118, B:D.250, B:E.251 GDP.15: 21 residues within 4Å: Chain E: G.115, A.116, G.117, K.118, T.119, T.120, R.146, Q.152, K.248, D.250, E.251, T.273, N.274, G.275, Q.276 Chain F: T.114 Chain G: Q.8 Ligands: MG.16, AF3.17, AF3.24, SO4.25 26 PLIP interactions: 20 interactions with chain E, 4 interactions with chain F, 2 interactions with chain G Hydrogen bonds: E:G.115, E:G.117, E:K.118, E:T.119, E:T.120, E:T.120, E:R.146, E:Q.152, E:Q.152, E:K.248, E:K.248, E:T.273, E:G.275, F:T.114, G:Q.8, G:Q.8 Water bridges: E:K.118, E:T.119, E:T.119, E:T.190, F:R.146, F:G.192, F:G.192 Salt bridges: E:K.118, E:D.250, E:E.251 GDP.22: 22 residues within 4Å: Chain E: T.114, R.146 Chain F: G.115, A.116, G.117, K.118, T.119, T.120, R.146, Q.152, K.248, D.250, E.251, T.273, N.274, G.275, Q.276 Chain H: Q.8 Ligands: AF3.17, SO4.18, MG.23, AF3.24 24 PLIP interactions: 21 interactions with chain F, 2 interactions with chain E, 1 interactions with chain H Hydrogen bonds: F:G.115, F:G.117, F:K.118, F:T.119, F:T.120, F:T.120, F:R.146, F:Q.152, F:Q.152, F:K.248, F:K.248, F:T.273, F:G.275, E:T.114, H:Q.8 Water bridges: F:K.118, F:T.119, F:T.119, F:T.119, F:Q.276, E:R.146 Salt bridges: F:K.118, F:D.250, F:E.251

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: T.119, D.143, D.189 Ligands: GDP.1, AF3.3 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.119, H2O.1, H2O.1 MG.10: 6 residues within 4Å: Chain B: T.119, D.143, D.189, T.190 Ligands: GDP.9, AF3.11 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.119, H2O.1, H2O.2, H2O.2 MG.16: 5 residues within 4Å: Chain E: T.119, D.143, D.189 Ligands: GDP.15, AF3.17 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:T.119, E:D.143, H2O.3, H2O.3 MG.23: 4 residues within 4Å: Chain F: T.119, D.143 Ligands: GDP.22, AF3.24 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:T.119, H2O.3, H2O.3

4 x AF3: ALUMINUM FLUORIDE(Non-covalent)

AF3.3: 10 residues within 4Å: Chain A: T.114, G.115, K.118, D.143, R.146, T.190, G.192 Ligands: GDP.1, MG.2, GDP.9 No protein-ligand interaction detected (PLIP) AF3.11: 9 residues within 4Å: Chain B: T.114, G.115, K.118, D.143, R.146, G.192 Ligands: GDP.1, GDP.9, MG.10 No protein-ligand interaction detected (PLIP) AF3.17: 10 residues within 4Å: Chain E: T.114, G.115, K.118, D.143, R.146, T.190, G.192 Ligands: GDP.15, MG.16, GDP.22 No protein-ligand interaction detected (PLIP) AF3.24: 9 residues within 4Å: Chain F: T.114, G.115, K.118, D.143, R.146, G.192 Ligands: GDP.15, GDP.22, MG.23 No protein-ligand interaction detected (PLIP)

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

SO4.4: 7 residues within 4Å: Chain A: Y.145, R.193, N.194, Y.200 Chain B: D.250, Q.276 Ligands: GDP.9 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Y.145, A:Y.145, A:N.194, B:Q.276 Salt bridges: A:R.193 Water bridges: B:Q.276, B:Q.276 SO4.5: 6 residues within 4Å: Chain A: K.225, Y.226, E.227, S.257 Chain B: K.225 Ligands: SO4.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.226, A:E.227 Water bridges: A:G.53 SO4.6: 3 residues within 4Å: Chain A: V.285, S.286, G.289 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.286, A:S.286, A:G.289 SO4.7: 5 residues within 4Å: Chain A: C.90, A.96, S.286, P.287, L.288 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.288 SO4.8: 4 residues within 4Å: Chain A: Y.107, K.177, S.212, S.213 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.213 Salt bridges: A:K.177 SO4.12: 5 residues within 4Å: Chain A: Q.276 Chain B: Y.145, R.193, N.194, Y.200 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:N.194, A:Q.276 Salt bridges: B:R.193 Water bridges: A:Q.276, A:Q.276 SO4.13: 6 residues within 4Å: Chain A: K.225 Chain B: A.224, K.225, Y.226, S.257 Ligands: SO4.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.224, B:Y.226 SO4.14: 4 residues within 4Å: Chain B: Y.107, K.177, S.212, S.213 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.212, B:S.213 Salt bridges: B:K.177 SO4.18: 6 residues within 4Å: Chain E: R.193, N.194, Y.200 Chain F: D.250, Q.276 Ligands: GDP.22 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:Q.276, F:Q.276, E:N.194 Salt bridges: E:R.193 SO4.19: 6 residues within 4Å: Chain E: A.224, K.225, Y.226, S.257 Chain F: K.225 Ligands: SO4.26 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Y.226 Water bridges: E:E.227 SO4.20: 4 residues within 4Å: Chain E: H.104, S.105, S.213, I.214 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:S.213, E:I.214 SO4.21: 4 residues within 4Å: Chain E: Y.107, K.177, S.212, S.213 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:S.213 Salt bridges: E:K.177 SO4.25: 7 residues within 4Å: Chain E: D.250, Q.276 Chain F: Y.145, R.193, N.194, Y.200 Ligands: GDP.15 5 PLIP interactions: 2 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:N.194, E:Q.276 Salt bridges: F:R.193 Water bridges: E:Q.276, E:Q.276 SO4.26: 6 residues within 4Å: Chain E: K.225 Chain F: A.224, K.225, Y.226, S.257 Ligands: SO4.19 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Y.226 Water bridges: F:S.257 SO4.27: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain F Salt bridges: F:H.134

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bange, G. et al., Structural basis for the molecular evolution of SRP-GTPase activation by protein. Nat.Struct.Mol.Biol. (2011)

Release Date

2011-11-09

Peptides

Flagellar biosynthesis protein flhF: ABEF
ATP-binding protein YlxH: CDGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
C

F
D

C
E

D
F

G
G

H
H

Flagellar biosynthesis protein flhF

ATP-binding protein YlxH

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