SMTL ID : 8eno.1

Homocitrate-deficient nitrogenase MoFe-protein from A. vinelandii nifV knockout in complex with NafT

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-1-mer

Ligands

2 x ICS: iron-sulfur-molybdenum cluster with interstitial carbon(Non-covalent)

ICS.1: 16 residues within 4Å: Chain A: V.67, R.93, Q.188, H.192, Y.226, I.228, C.272, S.275, I.352, G.353, G.354, L.355, R.356, F.378, H.439 Ligands: CIT.2 2 PLIP interactions: 2 interactions with chain A, Salt bridges: A:E.377 Metal complexes: A:C.272 ICS.6: 14 residues within 4Å: Chain C: V.67, R.93, Q.188, H.192, Y.226, C.272, R.274, S.275, I.352, G.353, G.354, L.355, R.356, H.439 1 PLIP interactions: 1 interactions with chain C, Metal complexes: C:C.272

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.2: 4 residues within 4Å: Chain A: R.93, Q.188, H.439 Ligands: ICS.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.188 Salt bridges: A:K.423, A:H.439, A:H.439

2 x CLF: FE(8)-S(7) CLUSTER(Non-covalent)

CLF.3: 19 residues within 4Å: Chain A: C.59, Y.61, P.82, G.84, C.85, Y.88, E.150, C.151, G.182 Chain B: C.69, P.71, S.91, G.93, C.94, Y.97, F.98, T.151, C.152, S.187 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B, Salt bridges: A:E.150 Metal complexes: A:C.59, A:C.85, A:C.85, A:C.151, B:C.69, B:C.94, B:C.94, B:C.152 CLF.8: 19 residues within 4Å: Chain C: C.59, Y.61, P.82, G.84, C.85, Y.88, E.150, C.151, G.182 Chain D: C.69, P.71, S.91, G.93, C.94, Y.97, F.98, T.151, C.152, S.187 9 PLIP interactions: 4 interactions with chain D, 5 interactions with chain C, Metal complexes: D:C.69, D:C.94, D:C.94, D:C.152, C:C.59, C:C.85, C:C.85, C:C.151 Salt bridges: C:E.150

2 x 1N7: CHAPSO(Non-covalent)

1N7.4: 10 residues within 4Å: Chain A: P.140, K.143 Chain B: E.32, K.33, Y.34, P.35, K.38, E.41, V.42, W.45 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.34, B:K.38, B:E.41, B:W.45, B:W.45, A:P.140 pi-Cation interactions: B:Y.34 1N7.9: 8 residues within 4Å: Chain C: P.140 Chain D: E.32, K.33, Y.34, K.38, E.41, V.42, W.45 8 PLIP interactions: 1 interactions with chain C, 7 interactions with chain D Hydrophobic interactions: C:P.140, D:K.38, D:W.45, D:W.45, D:W.45 Hydrogen bonds: D:E.32, D:E.32 pi-Cation interactions: D:Y.34

2 x FE: FE (III) ION(Non-covalent)

FE.5: 4 residues within 4Å: Chain B: D.352, D.356 Chain D: R.107, E.108 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain B Metal complexes: D:R.107, D:E.108, B:D.352, B:D.352, B:D.356 FE.7: 5 residues within 4Å: Chain A: K.430 Chain B: R.107, E.108 Chain D: D.352, D.356 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Metal complexes: D:D.352, D:D.356, B:R.107, B:E.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Warmack, R.A. et al., Structural consequences of turnover-induced homocitrate loss in nitrogenase. Nat Commun (2023)

Release Date

2023-03-08

Peptides

Nitrogenase molybdenum-iron protein alpha chain: AC
Nitrogenase molybdenum-iron protein beta chain: BD
nitrogenase-associated factor T: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

Nitrogenase molybdenum-iron protein alpha chain

Nitrogenase molybdenum-iron protein beta chain

nitrogenase-associated factor T

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