SMTL ID : 5bn3.1

Structure of a unique ATP synthase NeqA-NeqB in complex with ADP from Nanoarcheaum equitans

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-3-3-mer

Ligands

3 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 17 residues within 4Å: Chain A: P.224, F.225, G.226, S.227, G.228, K.229, T.230, V.231, Y.414, Q.491, D.492, A.493, F.494 Chain B: L.324, R.326 Ligands: GOL.7, MG.9 22 PLIP interactions: 18 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:G.226, A:S.227, A:G.228, A:K.229, A:T.230, A:V.231, A:Q.491, A:D.492, A:A.493 Water bridges: A:K.229, A:L.232, A:E.252, A:R.253, A:R.253, A:D.320, A:Y.414, B:R.326, B:A.328 Salt bridges: A:K.229, B:R.326, B:R.326 pi-Stacking: A:Y.414 ADP.23: 17 residues within 4Å: Chain C: P.224, F.225, G.226, S.227, G.228, K.229, T.230, V.231, Y.414, Q.491, D.492, A.493, F.494 Chain D: L.324, R.326 Ligands: GOL.29, MG.31 22 PLIP interactions: 18 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:G.226, C:S.227, C:G.228, C:K.229, C:T.230, C:V.231, C:Q.491, C:D.492, C:A.493 Water bridges: C:K.229, C:L.232, C:E.252, C:R.253, C:R.253, C:D.320, C:Y.414, D:R.326, D:A.328 Salt bridges: C:K.229, D:R.326, D:R.326 pi-Stacking: C:Y.414 ADP.45: 17 residues within 4Å: Chain E: P.224, F.225, G.226, S.227, G.228, K.229, T.230, V.231, Y.414, Q.491, D.492, A.493, F.494 Chain F: L.324, R.326 Ligands: GOL.51, MG.53 23 PLIP interactions: 19 interactions with chain E, 4 interactions with chain F Hydrogen bonds: E:G.226, E:S.227, E:G.228, E:K.229, E:T.230, E:T.230, E:V.231, E:Q.491, E:D.492, E:A.493 Water bridges: E:K.229, E:L.232, E:E.252, E:R.253, E:R.253, E:D.320, E:Y.414, F:R.326, F:A.328 Salt bridges: E:K.229, F:R.326, F:R.326 pi-Stacking: E:Y.414

24 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)

DIO.2: 5 residues within 4Å: Chain A: F.449 Chain D: H.310, S.311, N.313 Ligands: GOL.6 Ligand excluded by PLIP DIO.3: 7 residues within 4Å: Chain A: F.140, D.269, T.272, K.274, P.275, Y.278, R.279 Ligand excluded by PLIP DIO.4: 5 residues within 4Å: Chain A: D.405, K.407, L.408, N.418, Y.419 Ligand excluded by PLIP DIO.5: 7 residues within 4Å: Chain A: Q.392, I.421 Chain D: P.136, P.283, G.284, N.285, Q.307 Ligand excluded by PLIP DIO.11: 2 residues within 4Å: Chain B: S.333, K.334 Ligand excluded by PLIP DIO.12: 5 residues within 4Å: Chain B: Y.112, G.331, M.332, S.333, H.336 Ligand excluded by PLIP DIO.13: 4 residues within 4Å: Chain B: S.66, E.67, Y.212, K.217 Ligand excluded by PLIP DIO.14: 1 residues within 4Å: Chain B: K.243 Ligand excluded by PLIP DIO.24: 5 residues within 4Å: Chain C: F.449 Chain F: H.310, S.311, N.313 Ligands: GOL.28 Ligand excluded by PLIP DIO.25: 7 residues within 4Å: Chain C: F.140, D.269, T.272, K.274, P.275, Y.278, R.279 Ligand excluded by PLIP DIO.26: 5 residues within 4Å: Chain C: D.405, K.407, L.408, N.418, Y.419 Ligand excluded by PLIP DIO.27: 7 residues within 4Å: Chain C: Q.392, I.421 Chain F: P.136, P.283, G.284, N.285, Q.307 Ligand excluded by PLIP DIO.33: 2 residues within 4Å: Chain D: S.333, K.334 Ligand excluded by PLIP DIO.34: 5 residues within 4Å: Chain D: Y.112, G.331, M.332, S.333, H.336 Ligand excluded by PLIP DIO.35: 4 residues within 4Å: Chain D: S.66, E.67, Y.212, K.217 Ligand excluded by PLIP DIO.36: 1 residues within 4Å: Chain D: K.243 Ligand excluded by PLIP DIO.46: 5 residues within 4Å: Chain B: H.310, S.311, N.313 Chain E: F.449 Ligands: GOL.50 Ligand excluded by PLIP DIO.47: 7 residues within 4Å: Chain E: F.140, D.269, T.272, K.274, P.275, Y.278, R.279 Ligand excluded by PLIP DIO.48: 5 residues within 4Å: Chain E: D.405, K.407, L.408, N.418, Y.419 Ligand excluded by PLIP DIO.49: 7 residues within 4Å: Chain B: P.136, P.283, G.284, N.285, Q.307 Chain E: Q.392, I.421 Ligand excluded by PLIP DIO.55: 2 residues within 4Å: Chain F: S.333, K.334 Ligand excluded by PLIP DIO.56: 5 residues within 4Å: Chain F: Y.112, G.331, M.332, S.333, H.336 Ligand excluded by PLIP DIO.57: 4 residues within 4Å: Chain F: S.66, E.67, Y.212, K.217 Ligand excluded by PLIP DIO.58: 1 residues within 4Å: Chain F: K.243 Ligand excluded by PLIP

21 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 8 residues within 4Å: Chain A: F.211, S.422, Y.423, T.424, R.445, F.449 Chain D: H.310 Ligands: DIO.2 Ligand excluded by PLIP GOL.7: 7 residues within 4Å: Chain A: F.225, G.226, A.409, R.412, Y.414 Chain B: L.321 Ligands: ADP.1 Ligand excluded by PLIP GOL.8: 7 residues within 4Å: Chain A: N.197, Y.198, K.215, S.314, R.362, G.371, S.372 Ligand excluded by PLIP GOL.15: 6 residues within 4Å: Chain A: R.412 Chain B: A.121, H.122, L.324, S.325, I.344 Ligand excluded by PLIP GOL.16: 2 residues within 4Å: Chain B: S.366, K.367 Ligand excluded by PLIP GOL.17: 5 residues within 4Å: Chain B: R.249, D.286, T.288, H.289, V.290 Ligand excluded by PLIP GOL.18: 7 residues within 4Å: Chain A: N.288 Chain B: N.95, G.96, L.97, A.98, S.261, R.265 Ligand excluded by PLIP GOL.28: 8 residues within 4Å: Chain C: F.211, S.422, Y.423, T.424, R.445, F.449 Chain F: H.310 Ligands: DIO.24 Ligand excluded by PLIP GOL.29: 7 residues within 4Å: Chain C: F.225, G.226, A.409, R.412, Y.414 Chain D: L.321 Ligands: ADP.23 Ligand excluded by PLIP GOL.30: 7 residues within 4Å: Chain C: N.197, Y.198, K.215, S.314, R.362, G.371, S.372 Ligand excluded by PLIP GOL.37: 6 residues within 4Å: Chain C: R.412 Chain D: A.121, H.122, L.324, S.325, I.344 Ligand excluded by PLIP GOL.38: 2 residues within 4Å: Chain D: S.366, K.367 Ligand excluded by PLIP GOL.39: 5 residues within 4Å: Chain D: R.249, D.286, T.288, H.289, V.290 Ligand excluded by PLIP GOL.40: 7 residues within 4Å: Chain C: N.288 Chain D: N.95, G.96, L.97, A.98, S.261, R.265 Ligand excluded by PLIP GOL.50: 8 residues within 4Å: Chain B: H.310 Chain E: F.211, S.422, Y.423, T.424, R.445, F.449 Ligands: DIO.46 Ligand excluded by PLIP GOL.51: 7 residues within 4Å: Chain E: F.225, G.226, A.409, R.412, Y.414 Chain F: L.321 Ligands: ADP.45 Ligand excluded by PLIP GOL.52: 7 residues within 4Å: Chain E: N.197, Y.198, K.215, S.314, R.362, G.371, S.372 Ligand excluded by PLIP GOL.59: 6 residues within 4Å: Chain E: R.412 Chain F: A.121, H.122, L.324, S.325, I.344 Ligand excluded by PLIP GOL.60: 2 residues within 4Å: Chain F: S.366, K.367 Ligand excluded by PLIP GOL.61: 5 residues within 4Å: Chain F: R.249, D.286, T.288, H.289, V.290 Ligand excluded by PLIP GOL.62: 7 residues within 4Å: Chain E: N.288 Chain F: N.95, G.96, L.97, A.98, S.261, R.265 Ligand excluded by PLIP

15 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 5 residues within 4Å: Chain A: T.230, E.252, R.253, E.256 Ligands: ADP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.230, H2O.2, H2O.2, H2O.3, H2O.6 MG.10: 5 residues within 4Å: Chain A: G.216, V.315, S.372, L.373, T.374 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:V.315, A:S.372, A:T.374 MG.19: 1 residues within 4Å: Chain B: D.90 No protein-ligand interaction detected (PLIP) MG.20: 1 residues within 4Å: Chain B: Y.102 No protein-ligand interaction detected (PLIP) MG.21: 2 residues within 4Å: Chain B: R.92, D.93 No protein-ligand interaction detected (PLIP) MG.31: 5 residues within 4Å: Chain C: T.230, E.252, R.253, E.256 Ligands: ADP.23 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:T.230, H2O.18, H2O.19, H2O.19, H2O.23 MG.32: 5 residues within 4Å: Chain C: G.216, V.315, S.372, L.373, T.374 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:V.315, C:S.372, C:T.374 MG.41: 1 residues within 4Å: Chain D: D.90 No protein-ligand interaction detected (PLIP) MG.42: 1 residues within 4Å: Chain D: Y.102 No protein-ligand interaction detected (PLIP) MG.43: 2 residues within 4Å: Chain D: R.92, D.93 No protein-ligand interaction detected (PLIP) MG.53: 5 residues within 4Å: Chain E: T.230, E.252, R.253, E.256 Ligands: ADP.45 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:T.230, H2O.34, H2O.35, H2O.35, H2O.39 MG.54: 5 residues within 4Å: Chain E: G.216, V.315, S.372, L.373, T.374 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:V.315, E:S.372, E:T.374 MG.63: 1 residues within 4Å: Chain F: D.90 No protein-ligand interaction detected (PLIP) MG.64: 1 residues within 4Å: Chain F: Y.102 No protein-ligand interaction detected (PLIP) MG.65: 2 residues within 4Å: Chain F: R.92, D.93 No protein-ligand interaction detected (PLIP)

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

SO4.22: 4 residues within 4Å: Chain B: S.306, Q.307, D.308, K.322 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.307, B:D.308 Water bridges: B:S.306, B:D.308, B:K.322 Salt bridges: B:K.322 SO4.44: 4 residues within 4Å: Chain D: S.306, Q.307, D.308, K.322 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Q.307, D:D.308 Water bridges: D:S.306, D:D.308, D:K.322 Salt bridges: D:K.322 SO4.66: 4 residues within 4Å: Chain F: S.306, Q.307, D.308, K.322 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:Q.307, F:D.308 Water bridges: F:S.306, F:D.308, F:K.322 Salt bridges: F:K.322

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mohanty, S. et al., Structural Basis for a Unique ATP Synthase Core Complex from Nanoarcheaum equitans. J.Biol.Chem. (2015)

Release Date

2015-09-16

Peptides

V-type ATP synthase alpha chain: ACE
NEQ263: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

V-type ATP synthase alpha chain

NEQ263

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