SMTL ID : 2bl2.1

THE MEMBRANE ROTOR OF THE V-TYPE ATPASE FROM ENTEROCOCCUS HIRAE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-10-mer

Ligands

50 x LHG: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE(Non-functional Binders)(Non-covalent)

LHG.1: 2 residues within 4Å: Ligands: LHG.11, LHG.16 Ligand excluded by PLIP LHG.3: 16 residues within 4Å: Chain A: L.17, T.21, F.25, K.32, L.104, F.105, I.108 Chain B: K.32 Chain J: F.101, F.105 Ligands: LHG.5, LHG.6, LHG.9, LHG.13, LHG.14, LHG.79 Ligand excluded by PLIP LHG.4: 11 residues within 4Å: Chain A: M.1, M.2, F.14 Chain J: F.14, L.17, L.90, L.93 Ligands: LHG.9, LHG.77, LHG.79, LHG.80 Ligand excluded by PLIP LHG.5: 5 residues within 4Å: Ligands: LHG.3, LHG.6, LHG.9, LHG.10, LHG.79 Ligand excluded by PLIP LHG.6: 4 residues within 4Å: Ligands: LHG.3, LHG.5, LHG.14, LHG.16 Ligand excluded by PLIP LHG.9: 12 residues within 4Å: Chain A: M.2, F.14, L.17, L.90, L.93 Chain B: M.1, M.2, F.14 Ligands: LHG.3, LHG.4, LHG.5, LHG.23 Ligand excluded by PLIP LHG.10: 3 residues within 4Å: Ligands: LHG.5, LHG.11, LHG.80 Ligand excluded by PLIP LHG.11: 3 residues within 4Å: Ligands: LHG.1, LHG.10, LHG.74 Ligand excluded by PLIP LHG.13: 17 residues within 4Å: Chain A: F.101, F.105 Chain B: L.17, T.21, I.24, F.25, K.32, L.104, F.105, I.108 Chain C: K.32 Ligands: LHG.3, LHG.14, LHG.15, LHG.22, LHG.23, LHG.24 Ligand excluded by PLIP LHG.14: 5 residues within 4Å: Ligands: LHG.3, LHG.6, LHG.13, LHG.15, LHG.23 Ligand excluded by PLIP LHG.15: 4 residues within 4Å: Ligands: LHG.13, LHG.14, LHG.16, LHG.24 Ligand excluded by PLIP LHG.16: 4 residues within 4Å: Ligands: LHG.1, LHG.6, LHG.15, LHG.19 Ligand excluded by PLIP LHG.19: 3 residues within 4Å: Ligands: LHG.16, LHG.20, LHG.29 Ligand excluded by PLIP LHG.20: 3 residues within 4Å: Ligands: LHG.19, LHG.29, LHG.33 Ligand excluded by PLIP LHG.22: 14 residues within 4Å: Chain B: F.101, F.105 Chain C: L.17, T.21, F.25, K.32, L.104, F.105, I.108 Chain D: K.32 Ligands: LHG.13, LHG.24, LHG.27, LHG.32 Ligand excluded by PLIP LHG.23: 11 residues within 4Å: Chain B: M.2, F.14, L.90, L.93 Chain C: M.1, M.2, F.14 Ligands: LHG.9, LHG.13, LHG.14, LHG.27 Ligand excluded by PLIP LHG.24: 4 residues within 4Å: Ligands: LHG.13, LHG.15, LHG.22, LHG.27 Ligand excluded by PLIP LHG.27: 12 residues within 4Å: Chain C: M.2, F.14, L.17, L.90, L.93 Chain D: M.1, M.2, F.14 Ligands: LHG.22, LHG.23, LHG.24, LHG.36 Ligand excluded by PLIP LHG.29: 4 residues within 4Å: Ligands: LHG.19, LHG.20, LHG.34, LHG.39 Ligand excluded by PLIP LHG.32: 16 residues within 4Å: Chain C: F.101, F.105 Chain D: L.17, T.21, F.25, K.32, L.104, F.105, I.108 Chain E: K.32 Ligands: LHG.22, LHG.33, LHG.34, LHG.36, LHG.37, LHG.41 Ligand excluded by PLIP LHG.33: 4 residues within 4Å: Ligands: LHG.20, LHG.32, LHG.34, LHG.36 Ligand excluded by PLIP LHG.34: 5 residues within 4Å: Ligands: LHG.29, LHG.32, LHG.33, LHG.37, LHG.39 Ligand excluded by PLIP LHG.36: 12 residues within 4Å: Chain D: M.2, F.14, L.17, L.90, L.93 Chain E: M.1, M.2, F.14 Ligands: LHG.27, LHG.32, LHG.33, LHG.47 Ligand excluded by PLIP LHG.37: 4 residues within 4Å: Ligands: LHG.32, LHG.34, LHG.38, LHG.41 Ligand excluded by PLIP LHG.38: 4 residues within 4Å: Ligands: LHG.37, LHG.39, LHG.41, LHG.48 Ligand excluded by PLIP LHG.39: 4 residues within 4Å: Ligands: LHG.29, LHG.34, LHG.38, LHG.44 Ligand excluded by PLIP LHG.41: 16 residues within 4Å: Chain D: F.101, F.105 Chain E: L.17, T.21, F.25, K.32, L.104, F.105, I.108 Chain F: K.32 Ligands: LHG.32, LHG.37, LHG.38, LHG.46, LHG.47, LHG.48 Ligand excluded by PLIP LHG.44: 2 residues within 4Å: Ligands: LHG.39, LHG.57 Ligand excluded by PLIP LHG.46: 15 residues within 4Å: Chain E: F.101, F.105 Chain F: L.17, T.21, F.25, K.32, L.104, F.105, I.108 Chain G: K.32 Ligands: LHG.41, LHG.48, LHG.49, LHG.52, LHG.59 Ligand excluded by PLIP LHG.47: 10 residues within 4Å: Chain E: M.2, F.14, L.90, L.93 Chain F: M.1, M.2, F.14 Ligands: LHG.36, LHG.41, LHG.52 Ligand excluded by PLIP LHG.48: 5 residues within 4Å: Ligands: LHG.38, LHG.41, LHG.46, LHG.49, LHG.52 Ligand excluded by PLIP LHG.49: 4 residues within 4Å: Ligands: LHG.46, LHG.48, LHG.53, LHG.57 Ligand excluded by PLIP LHG.52: 12 residues within 4Å: Chain F: M.2, F.14, L.17, L.90, L.93 Chain G: M.1, M.2, F.14 Ligands: LHG.46, LHG.47, LHG.48, LHG.54 Ligand excluded by PLIP LHG.53: 3 residues within 4Å: Ligands: LHG.49, LHG.54, LHG.59 Ligand excluded by PLIP LHG.54: 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.52, LHG.53, LHG.59, LHG.71 Ligand excluded by PLIP LHG.56: 2 residues within 4Å: Ligands: LHG.57, LHG.66 Ligand excluded by PLIP LHG.57: 4 residues within 4Å: Ligands: LHG.44, LHG.49, LHG.56, LHG.63 Ligand excluded by PLIP LHG.59: 15 residues within 4Å: Chain F: F.101, F.105 Chain G: L.17, T.21, F.25, K.32, L.104, F.105, I.108 Chain H: K.32 Ligands: LHG.46, LHG.53, LHG.54, LHG.65, LHG.66 Ligand excluded by PLIP LHG.62: 3 residues within 4Å: Ligands: LHG.66, LHG.72, LHG.74 Ligand excluded by PLIP LHG.63: 1 residues within 4Å: Ligands: LHG.57 Ligand excluded by PLIP LHG.65: 16 residues within 4Å: Chain G: F.101, F.105 Chain H: L.17, T.21, I.24, F.25, K.32, L.104, F.105, I.108 Chain I: K.32 Ligands: LHG.59, LHG.66, LHG.70, LHG.71, LHG.72 Ligand excluded by PLIP LHG.66: 5 residues within 4Å: Ligands: LHG.56, LHG.59, LHG.62, LHG.65, LHG.71 Ligand excluded by PLIP LHG.70: 15 residues within 4Å: Chain H: F.101, F.105 Chain I: L.17, T.21, F.25, K.32, L.104, F.105, I.108 Chain J: K.32 Ligands: LHG.65, LHG.72, LHG.73, LHG.77, LHG.79 Ligand excluded by PLIP LHG.71: 12 residues within 4Å: Chain H: M.2, F.14, L.17, L.90, L.93 Chain I: M.1, M.2, L.5 Ligands: LHG.54, LHG.65, LHG.66, LHG.77 Ligand excluded by PLIP LHG.72: 4 residues within 4Å: Ligands: LHG.62, LHG.65, LHG.70, LHG.73 Ligand excluded by PLIP LHG.73: 4 residues within 4Å: Ligands: LHG.70, LHG.72, LHG.74, LHG.80 Ligand excluded by PLIP LHG.74: 3 residues within 4Å: Ligands: LHG.11, LHG.62, LHG.73 Ligand excluded by PLIP LHG.77: 11 residues within 4Å: Chain I: M.2, F.14, L.17, L.90, L.93 Chain J: M.1, M.2, F.14 Ligands: LHG.4, LHG.70, LHG.71 Ligand excluded by PLIP LHG.79: 16 residues within 4Å: Chain A: K.32 Chain I: F.101, F.105 Chain J: L.17, T.21, I.24, F.25, K.32, L.104, F.105, I.108 Ligands: LHG.3, LHG.4, LHG.5, LHG.70, LHG.80 Ligand excluded by PLIP LHG.80: 4 residues within 4Å: Ligands: LHG.4, LHG.10, LHG.73, LHG.79 Ligand excluded by PLIP

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

NA.2: 6 residues within 4Å: Chain A: L.61, P.62, 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:E.139 NA.12: 6 residues within 4Å: Chain B: L.61, P.62, 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.21: 6 residues within 4Å: Chain C: L.61, P.62, 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:E.139 NA.31: 6 residues within 4Å: Chain D: L.61, P.62, 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:E.139 NA.40: 6 residues within 4Å: Chain E: L.61, P.62, 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.45: 6 residues within 4Å: Chain F: L.61, P.62, T.64, Q.65, Q.110, E.139 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:T.64, F:Q.65, F:Q.65, F:Q.110, F:E.139 NA.58: 6 residues within 4Å: Chain G: L.61, P.62, 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.64: 6 residues within 4Å: Chain H: L.61, P.62, 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.69: 6 residues within 4Å: Chain I: L.61, P.62, T.64, Q.65, Q.110, E.139 4 PLIP interactions: 4 interactions with chain I Hydrogen bonds: I:T.64, I:Q.65, I:Q.110, I:Q.110 NA.78: 6 residues within 4Å: Chain J: L.61, P.62, T.64, Q.65, Q.110, E.139 5 PLIP interactions: 5 interactions with chain J Hydrogen bonds: J:L.61, J:T.64, J:Q.65, J:Q.65, J:Q.110

22 x UMQ: UNDECYL-MALTOSIDE(Non-covalent)(Non-functional Binders)

UMQ.7: 4 residues within 4Å: Chain A: G.53, Q.54, I.57, L.60 Ligand excluded by PLIP UMQ.8: 4 residues within 4Å: Chain A: E.50, F.52, G.53, Q.54 Ligand excluded by PLIP UMQ.17: 3 residues within 4Å: Chain B: G.53, I.57, L.60 Ligand excluded by PLIP UMQ.18: 4 residues within 4Å: Chain B: E.50, F.52, G.53, Q.54 Ligand excluded by PLIP UMQ.25: 4 residues within 4Å: Chain C: L.56, I.57, L.60 Ligands: UMQ.26 Ligand excluded by PLIP UMQ.26: 6 residues within 4Å: Chain C: E.50, F.52, G.53, Q.54, L.56 Ligands: UMQ.25 Ligand excluded by PLIP UMQ.28: 6 residues within 4Å: Chain C: Q.54, I.57, P.125, E.126, T.129, I.132 Ligand excluded by PLIP UMQ.30: 1 residues within 4Å: Ligands: UMQ.35 Ligand excluded by PLIP UMQ.35: 5 residues within 4Å: Chain D: E.50, F.52, G.53, Q.54 Ligands: UMQ.30 Ligand excluded by PLIP UMQ.42: 3 residues within 4Å: Chain E: Q.54, L.60 Ligands: UMQ.43 Ligand excluded by PLIP UMQ.43: 5 residues within 4Å: Chain E: E.50, G.53, Q.54, L.56 Ligands: UMQ.42 Ligand excluded by PLIP UMQ.50: 1 residues within 4Å: Chain F: I.57 Ligand excluded by PLIP UMQ.51: 4 residues within 4Å: Chain F: E.50, F.52, G.53, Q.54 Ligand excluded by PLIP UMQ.55: 6 residues within 4Å: Chain F: Q.54, L.61, P.125, E.126, T.129, I.132 Ligand excluded by PLIP UMQ.60: 4 residues within 4Å: Chain G: G.53, L.56, L.60 Ligands: UMQ.61 Ligand excluded by PLIP UMQ.61: 5 residues within 4Å: Chain G: E.50, F.52, G.53, Q.54 Ligands: UMQ.60 Ligand excluded by PLIP UMQ.67: 4 residues within 4Å: Chain H: G.53, Q.54, I.57, L.60 Ligand excluded by PLIP UMQ.68: 4 residues within 4Å: Chain H: E.50, F.52, G.53, Q.54 Ligand excluded by PLIP UMQ.75: 3 residues within 4Å: Chain I: Q.54, I.57, L.60 Ligand excluded by PLIP UMQ.76: 4 residues within 4Å: Chain I: E.50, F.52, G.53, L.56 Ligand excluded by PLIP UMQ.81: 3 residues within 4Å: Chain J: L.56, L.60 Ligands: UMQ.82 Ligand excluded by PLIP UMQ.82: 3 residues within 4Å: Chain I: I.133 Chain J: L.56 Ligands: UMQ.81 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murata, T. et al., Structure of the Rotor of the Vacuolar-Type Na- ATPase from Enterococcus Hirae. Science (2005)

Release Date

2005-04-05

Peptides

V-TYPE SODIUM ATP SYNTHASE 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 ATP SYNTHASE SUBUNIT K

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