SMTL ID : 2db4.1

Crystal structure of rotor ring with DCCD of the V- ATPase from Enterococcus hirae

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-10-mer

Ligands

10 x DCW: DICYCLOHEXYLUREA(Covalent)

DCW.1: 5 residues within 4Å: Chain A: T.64, A.136, E.139, T.140, I.143 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.64, A:A.136 Hydrogen bonds: A:A.136 Water bridges: A:T.64 DCW.8: 4 residues within 4Å: Chain B: T.64, A.136, E.139, T.140 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.64, B:A.136 Hydrogen bonds: B:A.136 DCW.13: 5 residues within 4Å: Chain C: T.64, A.136, E.139, T.140 Ligands: UMQ.16 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:T.64, C:A.136 Hydrogen bonds: C:A.136 DCW.20: 4 residues within 4Å: Chain D: T.64, A.136, E.139, T.140 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:T.64, D:A.136 Hydrogen bonds: D:A.136 Water bridges: D:Y.68 DCW.25: 5 residues within 4Å: Chain E: T.64, A.136, E.139, T.140, I.143 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:T.64, E:A.136 Hydrogen bonds: E:A.136 DCW.31: 6 residues within 4Å: Chain F: T.64, A.136, E.139, T.140, I.143 Ligands: UMQ.30 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:T.64, F:A.136 Hydrogen bonds: F:A.136 Water bridges: F:T.64, F:Y.68 DCW.35: 5 residues within 4Å: Chain G: T.64, A.136, E.139, T.140, I.143 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:T.64, G:A.136 Hydrogen bonds: G:A.136 Water bridges: G:T.64 DCW.39: 5 residues within 4Å: Chain H: T.64, A.136, E.139, T.140, I.143 4 PLIP interactions: 4 interactions with chain H Hydrophobic interactions: H:T.64, H:A.136 Hydrogen bonds: H:A.136 Water bridges: H:T.64 DCW.44: 5 residues within 4Å: Chain I: T.64, A.136, E.139, T.140, I.143 4 PLIP interactions: 4 interactions with chain I Hydrophobic interactions: I:T.64, I:A.136 Hydrogen bonds: I:A.136 Water bridges: I:T.64 DCW.50: 5 residues within 4Å: Chain J: T.64, A.136, E.139, T.140, I.143 3 PLIP interactions: 3 interactions with chain J Hydrophobic interactions: J:T.64 Hydrogen bonds: J:A.136 Water bridges: J:T.64

10 x NA: SODIUM ION(Non-functional Binders)

NA.2: 7 residues within 4Å: Chain A: L.61, P.62, G.63, T.64, Q.65, Q.110, E.139 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.64, A:Q.65, A:Q.65, A:Q.110, A:Q.110 NA.7: 7 residues within 4Å: Chain B: L.61, P.62, G.63, T.64, Q.65, Q.110, E.139 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.64, B:Q.65, B:Q.65, B:Q.110, B:Q.110 NA.11: 7 residues within 4Å: Chain C: L.61, P.62, G.63, T.64, Q.65, Q.110, E.139 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.64, C:Q.65, C:Q.65, C:Q.110, C:Q.110 NA.17: 7 residues within 4Å: Chain D: L.61, P.62, G.63, T.64, Q.65, Q.110, E.139 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.64, D:Q.65, D:Q.65, D:Q.110, D:Q.110 NA.22: 7 residues within 4Å: Chain E: L.61, P.62, G.63, T.64, Q.65, Q.110, E.139 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:T.64, E:Q.65, E:Q.65, E:Q.110, E:Q.110 NA.26: 7 residues within 4Å: Chain F: L.61, P.62, G.63, T.64, Q.65, Q.110, E.139 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:P.62, F:T.64, F:Q.65, F:Q.65, F:Q.110 NA.32: 7 residues within 4Å: Chain G: L.61, P.62, G.63, T.64, Q.65, Q.110, E.139 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:T.64, G:Q.65, G:Q.65, G:Q.110, G:Q.110 NA.36: 7 residues within 4Å: Chain H: L.61, P.62, G.63, T.64, Q.65, Q.110, E.139 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:T.64, H:Q.65, H:Q.65, H:Q.110, H:Q.110 NA.40: 7 residues within 4Å: Chain I: L.61, P.62, G.63, T.64, Q.65, Q.110, E.139 5 PLIP interactions: 5 interactions with chain I Hydrogen bonds: I:T.64, I:T.64, I:Q.65, I:Q.65, I:Q.110 NA.45: 7 residues within 4Å: Chain J: L.61, P.62, G.63, T.64, Q.65, Q.110, E.139 5 PLIP interactions: 5 interactions with chain J Hydrogen bonds: J:T.64, J:T.64, J:Q.65, J:Q.65, J:Q.110

20 x LHG: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE(Non-covalent)

LHG.3: 13 residues within 4Å: Chain A: L.17, T.21, F.25, K.32, L.97, F.101, L.104, F.105, I.108 Chain J: F.101, F.105 Ligands: LHG.10, LHG.14 Ligand excluded by PLIP LHG.4: 10 residues within 4Å: Chain A: M.1, M.2, F.14 Chain J: L.17, L.90, L.93 Ligands: LHG.10, LHG.41, LHG.46, LHG.47 Ligand excluded by PLIP LHG.9: 10 residues within 4Å: Chain A: F.101, F.105 Chain B: L.17, T.21, F.25, K.32, L.97, L.104, F.105 Ligands: LHG.14 Ligand excluded by PLIP LHG.10: 10 residues within 4Å: Chain A: M.2, L.17, L.90, L.93 Chain B: M.1, M.2 Ligands: LHG.3, LHG.4, LHG.14, LHG.46 Ligand excluded by PLIP LHG.12: 13 residues within 4Å: Chain B: F.101, F.105 Chain C: L.17, T.21, F.25, K.32, L.97, F.101, L.104, F.105, I.108 Ligands: LHG.18, LHG.23 Ligand excluded by PLIP LHG.14: 10 residues within 4Å: Chain B: M.2, L.90, L.93 Chain C: M.1, M.2, F.14 Ligands: LHG.3, LHG.9, LHG.10, LHG.18 Ligand excluded by PLIP LHG.15: 10 residues within 4Å: Chain C: F.101, F.105 Chain D: L.17, T.21, F.25, K.32, L.97, L.104, F.105 Ligands: LHG.23 Ligand excluded by PLIP LHG.18: 9 residues within 4Å: Chain C: M.2, L.17, L.90, L.93 Chain D: M.1, M.2 Ligands: LHG.12, LHG.14, LHG.23 Ligand excluded by PLIP LHG.19: 10 residues within 4Å: Chain D: F.101, F.105 Chain E: L.17, T.21, F.25, K.32, L.97, L.104, F.105 Ligands: LHG.28 Ligand excluded by PLIP LHG.23: 11 residues within 4Å: Chain D: M.2, F.14, L.17, L.90, L.93 Chain E: M.1, M.2 Ligands: LHG.12, LHG.15, LHG.18, LHG.28 Ligand excluded by PLIP LHG.27: 12 residues within 4Å: Chain E: F.101, F.105 Chain F: L.17, T.21, F.25, L.97, F.101, L.104, F.105, I.108 Ligands: LHG.33, LHG.37 Ligand excluded by PLIP LHG.28: 9 residues within 4Å: Chain E: M.2, L.90, L.93 Chain F: M.1, M.2, F.14 Ligands: LHG.19, LHG.23, LHG.33 Ligand excluded by PLIP LHG.29: 12 residues within 4Å: Chain F: F.101, F.105 Chain G: L.17, T.21, F.25, K.32, L.97, F.101, L.104, F.105 Ligands: LHG.37, LHG.42 Ligand excluded by PLIP LHG.33: 9 residues within 4Å: Chain F: M.2, L.17, L.90, L.93 Chain G: M.1, M.2 Ligands: LHG.27, LHG.28, LHG.37 Ligand excluded by PLIP LHG.34: 11 residues within 4Å: Chain G: F.101, F.105 Chain H: L.17, T.21, F.25, K.32, L.97, F.101, L.104, F.105 Ligands: LHG.42 Ligand excluded by PLIP LHG.37: 12 residues within 4Å: Chain G: M.2, F.14, L.17, L.90, L.93 Chain H: M.1, M.2, F.14 Ligands: LHG.27, LHG.29, LHG.33, LHG.42 Ligand excluded by PLIP LHG.41: 11 residues within 4Å: Chain H: F.101, F.105 Chain I: L.17, T.21, F.25, F.101, L.104, F.105, I.108 Ligands: LHG.4, LHG.47 Ligand excluded by PLIP LHG.42: 10 residues within 4Å: Chain H: M.2, L.17, L.90, L.93 Chain I: M.1, M.2 Ligands: LHG.29, LHG.34, LHG.37, LHG.47 Ligand excluded by PLIP LHG.46: 12 residues within 4Å: Chain I: F.101, F.105 Chain J: L.17, T.21, F.25, K.32, F.101, L.104, F.105, I.108 Ligands: LHG.4, LHG.10 Ligand excluded by PLIP LHG.47: 10 residues within 4Å: Chain I: M.2, F.14, L.17, L.90, L.93 Chain J: M.1, M.2 Ligands: LHG.4, LHG.41, LHG.42 Ligand excluded by PLIP

10 x UMQ: UNDECYL-MALTOSIDE(Non-covalent)

UMQ.5: 5 residues within 4Å: Chain A: G.53, Q.54, L.56, I.57, L.60 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.56, A:I.57, A:L.60 Hydrogen bonds: A:Q.54 UMQ.6: 4 residues within 4Å: Chain A: E.50, F.52, G.53, Q.54 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.52 Hydrogen bonds: A:E.50, A:F.52, A:G.53, A:Q.54 UMQ.16: 8 residues within 4Å: Chain C: Q.54, I.57, P.125, E.126, A.128, T.129, I.132 Ligands: DCW.13 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.57, C:I.132, C:I.132 Hydrogen bonds: C:Q.54 UMQ.21: 5 residues within 4Å: Chain C: I.133 Chain D: E.50, F.52, G.53, Q.54 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.52, C:I.133 Hydrogen bonds: D:E.50, D:G.53, D:Q.54 UMQ.24: 5 residues within 4Å: Chain E: E.50, F.52, G.53, Q.54, L.56 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:L.56 Hydrogen bonds: E:G.53, E:Q.54 UMQ.30: 8 residues within 4Å: Chain F: Q.54, L.60, P.125, E.126, A.128, T.129, I.132 Ligands: DCW.31 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:L.60, F:I.132 Hydrogen bonds: F:Q.54, F:T.129 UMQ.38: 5 residues within 4Å: Chain H: E.50, F.52, G.53, Q.54, L.56 6 PLIP interactions: 6 interactions with chain H Hydrophobic interactions: H:F.52, H:F.52, H:L.56 Hydrogen bonds: H:E.50, H:G.53, H:Q.54 UMQ.43: 2 residues within 4Å: Chain I: E.50, G.53 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:E.50, I:G.53 UMQ.48: 3 residues within 4Å: Chain J: L.56, L.60 Ligands: UMQ.49 2 PLIP interactions: 2 interactions with chain J Hydrophobic interactions: J:L.56, J:L.60 UMQ.49: 4 residues within 4Å: Chain I: M.137 Chain J: F.52, L.56 Ligands: UMQ.48 3 PLIP interactions: 3 interactions with chain J Hydrophobic interactions: J:F.52, J:L.56 Water bridges: J:G.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mizutani, K. et al., Structure of the rotor ring modified with N,N'-dicyclohexylcarbodiimide of the Na+-transporting vacuolar ATPase. Proc.Natl.Acad.Sci.USA (2011)

Release Date

2006-12-05

Peptides

V-Type Sodium ATPase Subunit K: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

Membrane

We predict this structure to be a membrane protein.
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V-Type Sodium ATPase Subunit K

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