SMTL ID : 2gj3.3 (5 other biounits)

Crystal structure of the FAD-containing PAS domain of the protein NifL from Azotobacter vinelandii.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.04 Å

Oligo State

homo-hexamer

Ligands

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

SO4.1: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.102 SO4.2: 5 residues within 4Å: Chain A: K.87 Chain C: R.69, Q.72, K.74 Ligands: SO4.3 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:Q.72 Salt bridges: C:R.69, C:K.74, A:K.87 Water bridges: A:K.87 SO4.3: 4 residues within 4Å: Chain A: K.87 Chain C: R.69, K.74 Ligands: SO4.2 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain C Water bridges: A:K.87, A:K.87, C:R.69 Salt bridges: A:K.87, C:R.69, C:K.74 SO4.5: 2 residues within 4Å: Chain B: N.101, E.102 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.102 Water bridges: B:N.101, B:A.103 SO4.8: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.102 SO4.9: 5 residues within 4Å: Chain C: K.87 Chain E: R.69, Q.72, K.74 Ligands: SO4.10 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain C Hydrogen bonds: E:Q.72 Salt bridges: E:R.69, E:K.74, C:K.87 Water bridges: C:K.87 SO4.10: 4 residues within 4Å: Chain C: K.87 Chain E: R.69, K.74 Ligands: SO4.9 6 PLIP interactions: 3 interactions with chain E, 3 interactions with chain C Water bridges: E:R.69, C:K.87, C:K.87 Salt bridges: E:R.69, E:K.74, C:K.87 SO4.12: 2 residues within 4Å: Chain D: N.101, E.102 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.102 Water bridges: D:N.101, D:A.103 SO4.15: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.102 SO4.16: 5 residues within 4Å: Chain A: R.69, Q.72, K.74 Chain E: K.87 Ligands: SO4.17 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:Q.72 Salt bridges: A:R.69, A:K.74, E:K.87 Water bridges: E:K.87 SO4.17: 4 residues within 4Å: Chain A: R.69, K.74 Chain E: K.87 Ligands: SO4.16 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain E Water bridges: A:R.69, E:K.87, E:K.87 Salt bridges: A:R.69, A:K.74, E:K.87 SO4.19: 2 residues within 4Å: Chain F: N.101, E.102 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:E.102 Water bridges: F:N.101, F:A.103

6 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.4: 20 residues within 4Å: Chain A: T.21, L.23, K.24, A.25, N.49, E.50, S.51, L.53, S.54, R.60, Y.63, W.67, L.70, L.80, N.82, L.94, V.96, Y.109, L.110, G.111 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:T.21, A:A.25, A:E.50, A:E.50, A:W.67, A:L.70, A:V.96 Hydrogen bonds: A:N.49, A:E.50, A:S.51, A:S.54, A:Y.63, A:W.67, A:N.82, A:N.82 Water bridges: A:N.49, A:S.54, A:N.55, A:R.60, A:R.60, A:H.113 Salt bridges: A:R.60, A:R.60 pi-Stacking: A:W.67, A:W.67, A:W.67 FAD.6: 19 residues within 4Å: Chain B: T.21, A.25, N.49, E.50, S.51, L.53, S.54, R.60, Y.63, Q.64, W.67, L.70, L.80, N.82, L.94, V.96, Y.109, L.110, G.111 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:T.21, B:A.25, B:E.50, B:L.70, B:V.96, B:Y.109, B:Y.109 Hydrogen bonds: B:S.51, B:S.51, B:S.54, B:S.54, B:R.60, B:N.82, B:N.82 Water bridges: B:Q.64 Salt bridges: B:R.60 pi-Stacking: B:W.67, B:W.67, B:W.67 FAD.11: 20 residues within 4Å: Chain C: T.21, L.23, K.24, A.25, N.49, E.50, S.51, L.53, S.54, R.60, Y.63, W.67, L.70, L.80, N.82, L.94, V.96, Y.109, L.110, G.111 26 PLIP interactions: 26 interactions with chain C Hydrophobic interactions: C:T.21, C:A.25, C:E.50, C:E.50, C:W.67, C:L.70, C:V.96 Hydrogen bonds: C:N.49, C:E.50, C:S.51, C:S.54, C:Y.63, C:W.67, C:N.82, C:N.82 Water bridges: C:N.49, C:S.54, C:N.55, C:R.60, C:R.60, C:H.113 Salt bridges: C:R.60, C:R.60 pi-Stacking: C:W.67, C:W.67, C:W.67 FAD.13: 19 residues within 4Å: Chain D: T.21, A.25, N.49, E.50, S.51, L.53, S.54, R.60, Y.63, Q.64, W.67, L.70, L.80, N.82, L.94, V.96, Y.109, L.110, G.111 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:T.21, D:A.25, D:E.50, D:L.70, D:V.96, D:Y.109, D:Y.109 Hydrogen bonds: D:S.51, D:S.51, D:S.54, D:S.54, D:R.60, D:N.82, D:N.82 Water bridges: D:Q.64 Salt bridges: D:R.60 pi-Stacking: D:W.67, D:W.67, D:W.67 FAD.18: 20 residues within 4Å: Chain E: T.21, L.23, K.24, A.25, N.49, E.50, S.51, L.53, S.54, R.60, Y.63, W.67, L.70, L.80, N.82, L.94, V.96, Y.109, L.110, G.111 26 PLIP interactions: 26 interactions with chain E Hydrophobic interactions: E:T.21, E:A.25, E:E.50, E:E.50, E:W.67, E:L.70, E:V.96 Hydrogen bonds: E:N.49, E:E.50, E:S.51, E:S.54, E:Y.63, E:W.67, E:N.82, E:N.82 Water bridges: E:N.49, E:S.54, E:N.55, E:R.60, E:R.60, E:H.113 Salt bridges: E:R.60, E:R.60 pi-Stacking: E:W.67, E:W.67, E:W.67 FAD.20: 19 residues within 4Å: Chain F: T.21, A.25, N.49, E.50, S.51, L.53, S.54, R.60, Y.63, Q.64, W.67, L.70, L.80, N.82, L.94, V.96, Y.109, L.110, G.111 19 PLIP interactions: 19 interactions with chain F Hydrophobic interactions: F:T.21, F:A.25, F:E.50, F:L.70, F:V.96, F:Y.109, F:Y.109 Hydrogen bonds: F:S.51, F:S.51, F:S.54, F:S.54, F:R.60, F:N.82, F:N.82 Water bridges: F:Q.64 Salt bridges: F:R.60 pi-Stacking: F:W.67, F:W.67, F:W.67

3 x EOH: ETHANOL(Non-functional Binders)

EOH.7: 1 residues within 4Å: Chain B: H.13 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:H.13 EOH.14: 1 residues within 4Å: Chain D: H.13 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:H.13 EOH.21: 1 residues within 4Å: Chain F: H.13 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:H.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Key, J. et al., Structure of the redox sensor domain of Azotobacter vinelandii NifL at atomic resolution: signaling, dimerization, and mechanism. Biochemistry (2007)

Release Date

2007-03-06

Peptides

Nitrogen fixation regulatory protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Nitrogen fixation regulatory protein

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