SMTL ID : 2gj3.2 (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-12-mer

Ligands

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

SO4.1: 3 residues within 4Å: Chain C: R.35, G.41, S.42 Ligand excluded by PLIP SO4.2: 3 residues within 4Å: Chain A: K.87 Ligands: SO4.3, SO4.23 Ligand excluded by PLIP SO4.3: 2 residues within 4Å: Chain A: K.87 Ligands: SO4.2 Ligand excluded by PLIP SO4.5: 7 residues within 4Å: Chain B: N.101, E.102 Chain D: N.101, E.102 Chain F: E.102 Ligands: SO4.12, SO4.19 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain E: R.35, G.41, S.42 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain C: K.87 Ligands: SO4.10, SO4.37 Ligand excluded by PLIP SO4.10: 2 residues within 4Å: Chain C: K.87 Ligands: SO4.9 Ligand excluded by PLIP SO4.12: 7 residues within 4Å: Chain B: E.102 Chain D: N.101, E.102 Chain F: N.101, E.102 Ligands: SO4.5, SO4.19 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain A: R.35, G.41, S.42 Ligand excluded by PLIP SO4.16: 3 residues within 4Å: Chain E: K.87 Ligands: SO4.17, SO4.30 Ligand excluded by PLIP SO4.17: 2 residues within 4Å: Chain E: K.87 Ligands: SO4.16 Ligand excluded by PLIP SO4.19: 7 residues within 4Å: Chain B: N.101, E.102 Chain D: E.102 Chain F: N.101, E.102 Ligands: SO4.5, SO4.12 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain I: R.35, G.41, S.42 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain G: K.87 Ligands: SO4.2, SO4.24 Ligand excluded by PLIP SO4.24: 2 residues within 4Å: Chain G: K.87 Ligands: SO4.23 Ligand excluded by PLIP SO4.26: 7 residues within 4Å: Chain H: N.101, E.102 Chain J: N.101, E.102 Chain L: E.102 Ligands: SO4.33, SO4.40 Ligand excluded by PLIP SO4.29: 3 residues within 4Å: Chain K: R.35, G.41, S.42 Ligand excluded by PLIP SO4.30: 3 residues within 4Å: Chain I: K.87 Ligands: SO4.16, SO4.31 Ligand excluded by PLIP SO4.31: 2 residues within 4Å: Chain I: K.87 Ligands: SO4.30 Ligand excluded by PLIP SO4.33: 7 residues within 4Å: Chain H: E.102 Chain J: N.101, E.102 Chain L: N.101, E.102 Ligands: SO4.26, SO4.40 Ligand excluded by PLIP SO4.36: 3 residues within 4Å: Chain G: R.35, G.41, S.42 Ligand excluded by PLIP SO4.37: 3 residues within 4Å: Chain K: K.87 Ligands: SO4.9, SO4.38 Ligand excluded by PLIP SO4.38: 2 residues within 4Å: Chain K: K.87 Ligands: SO4.37 Ligand excluded by PLIP SO4.40: 7 residues within 4Å: Chain H: N.101, E.102 Chain J: E.102 Chain L: N.101, E.102 Ligands: SO4.26, SO4.33 Ligand excluded by PLIP

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

FAD.4: 24 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 Chain K: L.23, A.71, K.73, E.105 34 PLIP interactions: 29 interactions with chain A, 5 interactions with chain K 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, K:A.71 Water bridges: A:N.49, A:S.54, A:N.55, A:R.60, A:R.60, A:R.60, A:R.60, A:R.60, A:H.113, K:T.106, K:Y.109, K:Y.109 Salt bridges: A:R.60, A:R.60, K:K.73 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: 24 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 Chain I: L.23, A.71, K.73, E.105 34 PLIP interactions: 29 interactions with chain C, 5 interactions with chain I 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, I:A.71 Water bridges: C:N.49, C:S.54, C:N.55, C:R.60, C:R.60, C:R.60, C:R.60, C:R.60, C:H.113, I:T.106, I:Y.109, I:Y.109 Salt bridges: C:R.60, C:R.60, I:K.73 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: 24 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 Chain G: L.23, A.71, K.73, E.105 34 PLIP interactions: 29 interactions with chain E, 5 interactions with chain G 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, G:A.71 Water bridges: E:N.49, E:S.54, E:N.55, E:R.60, E:R.60, E:R.60, E:R.60, E:R.60, E:H.113, G:T.106, G:Y.109, G:Y.109 Salt bridges: E:R.60, E:R.60, G:K.73 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 FAD.25: 24 residues within 4Å: Chain E: L.23, A.71, K.73, E.105 Chain G: 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 31 PLIP interactions: 27 interactions with chain G, 4 interactions with chain E Hydrophobic interactions: G:T.21, G:A.25, G:E.50, G:E.50, G:W.67, G:L.70, G:V.96 Hydrogen bonds: G:N.49, G:E.50, G:S.51, G:S.54, G:W.67, G:N.82, G:N.82, E:A.71 Water bridges: G:N.49, G:S.54, G:N.55, G:R.60, G:R.60, G:R.60, G:R.60, G:R.60, E:E.105, E:Y.109 Salt bridges: G:R.60, G:R.60, E:K.73 pi-Stacking: G:W.67, G:W.67, G:W.67 FAD.27: 19 residues within 4Å: Chain H: 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 20 PLIP interactions: 20 interactions with chain H Hydrophobic interactions: H:T.21, H:A.25, H:E.50, H:L.70, H:V.96, H:Y.109, H:Y.109 Hydrogen bonds: H:S.51, H:S.51, H:S.54, H:S.54, H:R.60, H:Y.63, H:N.82, H:N.82 Water bridges: H:Q.64 Salt bridges: H:R.60 pi-Stacking: H:W.67, H:W.67, H:W.67 FAD.32: 24 residues within 4Å: Chain C: L.23, A.71, K.73, E.105 Chain I: 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 31 PLIP interactions: 27 interactions with chain I, 4 interactions with chain C Hydrophobic interactions: I:T.21, I:A.25, I:E.50, I:E.50, I:W.67, I:L.70, I:V.96 Hydrogen bonds: I:N.49, I:E.50, I:S.51, I:S.54, I:W.67, I:N.82, I:N.82, C:A.71 Water bridges: I:N.49, I:S.54, I:N.55, I:R.60, I:R.60, I:R.60, I:R.60, I:R.60, C:E.105, C:Y.109 Salt bridges: I:R.60, I:R.60, C:K.73 pi-Stacking: I:W.67, I:W.67, I:W.67 FAD.34: 19 residues within 4Å: Chain J: 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 20 PLIP interactions: 20 interactions with chain J Hydrophobic interactions: J:T.21, J:A.25, J:E.50, J:L.70, J:V.96, J:Y.109, J:Y.109 Hydrogen bonds: J:S.51, J:S.51, J:S.54, J:S.54, J:R.60, J:Y.63, J:N.82, J:N.82 Water bridges: J:Q.64 Salt bridges: J:R.60 pi-Stacking: J:W.67, J:W.67, J:W.67 FAD.39: 24 residues within 4Å: Chain A: L.23, A.71, K.73, E.105 Chain K: 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 31 PLIP interactions: 27 interactions with chain K, 4 interactions with chain A Hydrophobic interactions: K:T.21, K:A.25, K:E.50, K:E.50, K:W.67, K:L.70, K:V.96 Hydrogen bonds: K:N.49, K:E.50, K:S.51, K:S.54, K:W.67, K:N.82, K:N.82, A:A.71 Water bridges: K:N.49, K:S.54, K:N.55, K:R.60, K:R.60, K:R.60, K:R.60, K:R.60, A:E.105, A:Y.109 Salt bridges: K:R.60, K:R.60, A:K.73 pi-Stacking: K:W.67, K:W.67, K:W.67 FAD.41: 19 residues within 4Å: Chain L: 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 20 PLIP interactions: 20 interactions with chain L Hydrophobic interactions: L:T.21, L:A.25, L:E.50, L:L.70, L:V.96, L:Y.109, L:Y.109 Hydrogen bonds: L:S.51, L:S.51, L:S.54, L:S.54, L:R.60, L:Y.63, L:N.82, L:N.82 Water bridges: L:Q.64 Salt bridges: L:R.60 pi-Stacking: L:W.67, L:W.67, L:W.67

6 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 EOH.28: 1 residues within 4Å: Chain H: H.13 2 PLIP interactions: 2 interactions with chain H Hydrophobic interactions: H:H.13 Hydrogen bonds: H:H.13 EOH.35: 1 residues within 4Å: Chain J: H.13 2 PLIP interactions: 2 interactions with chain J Hydrophobic interactions: J:H.13 Hydrogen bonds: J:H.13 EOH.42: 1 residues within 4Å: Chain L: H.13 2 PLIP interactions: 2 interactions with chain L Hydrophobic interactions: L:H.13 Hydrogen bonds: L: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: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

I
A

J
B

K
A

L
B

Nitrogen fixation regulatory protein

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