SMTL ID : 2cyd.1

Crystal structure of Lithium bound rotor ring of the V-ATPase from Enterococcus hirae

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-10-mer

Ligands

10 x LI: LITHIUM ION(Non-covalent)

LI.1: 6 residues within 4Å: Chain A: L.61, P.62, T.64, Q.65, Q.110, E.139 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:L.61, A:T.64, A:E.139 LI.4: 6 residues within 4Å: Chain B: L.61, P.62, T.64, Q.65, Q.110, E.139 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:L.61, B:T.64, B:E.139 LI.7: 6 residues within 4Å: Chain C: L.61, P.62, T.64, Q.65, Q.110, E.139 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:L.61, C:T.64, C:E.139 LI.11: 6 residues within 4Å: Chain D: L.61, P.62, T.64, Q.65, Q.110, E.139 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:L.61, D:T.64, D:E.139 LI.14: 6 residues within 4Å: Chain E: L.61, P.62, T.64, Q.65, Q.110, E.139 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:L.61, E:T.64, E:E.139 LI.17: 6 residues within 4Å: Chain F: L.61, P.62, T.64, Q.65, Q.110, E.139 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:L.61, F:T.64, F:E.139 LI.21: 6 residues within 4Å: Chain G: L.61, P.62, T.64, Q.65, Q.110, E.139 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:L.61, G:T.64, G:E.139 LI.24: 6 residues within 4Å: Chain H: L.61, P.62, T.64, Q.65, Q.110, E.139 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:L.61, H:T.64, H:E.139 LI.27: 6 residues within 4Å: Chain I: L.61, P.62, T.64, Q.65, Q.110, E.139 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:L.61, I:T.64, I:E.139 LI.30: 6 residues within 4Å: Chain J: L.61, P.62, T.64, Q.65, Q.110, E.139 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:L.61, J:T.64, J:E.139

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

LHG.2: 12 residues within 4Å: Chain A: L.17, T.21, F.25, K.32, L.104, F.105 Chain B: K.32 Chain J: F.101, F.105 Ligands: LHG.5, LHG.6, LHG.31 Ligand excluded by PLIP LHG.3: 9 residues within 4Å: Chain A: M.1, M.2 Chain J: F.14, L.17, L.93 Ligands: LHG.6, LHG.28, LHG.31, LHG.32 Ligand excluded by PLIP LHG.5: 13 residues within 4Å: Chain A: F.101, F.105 Chain B: L.17, T.21, F.25, K.32, L.104, F.105, I.108 Chain C: K.32 Ligands: LHG.2, LHG.8, LHG.9 Ligand excluded by PLIP LHG.6: 10 residues within 4Å: Chain A: M.2, F.14, L.17, L.93 Chain B: M.1, M.2 Ligands: LHG.2, LHG.3, LHG.9, LHG.31 Ligand excluded by PLIP LHG.8: 13 residues within 4Å: Chain B: F.101, F.105 Chain C: L.17, T.21, F.25, K.32, L.104, F.105 Chain D: K.32 Ligands: LHG.5, LHG.12, LHG.13, LHG.16 Ligand excluded by PLIP LHG.9: 9 residues within 4Å: Chain B: M.2, F.14, L.17, L.93 Chain C: M.1, M.2 Ligands: LHG.5, LHG.6, LHG.13 Ligand excluded by PLIP LHG.12: 12 residues within 4Å: Chain C: F.101, F.105 Chain D: L.17, T.21, F.25, K.32, L.104, F.105 Chain E: K.32 Ligands: LHG.8, LHG.15, LHG.16 Ligand excluded by PLIP LHG.13: 9 residues within 4Å: Chain C: M.2, F.14, L.17, L.93 Chain D: M.1, M.2 Ligands: LHG.8, LHG.9, LHG.16 Ligand excluded by PLIP LHG.15: 12 residues within 4Å: Chain D: F.101, F.105 Chain E: L.17, T.21, F.25, K.32, L.104, F.105 Chain F: K.32 Ligands: LHG.12, LHG.18, LHG.19 Ligand excluded by PLIP LHG.16: 10 residues within 4Å: Chain D: M.2, F.14, L.17, L.93 Chain E: M.1, M.2 Ligands: LHG.8, LHG.12, LHG.13, LHG.19 Ligand excluded by PLIP LHG.18: 13 residues within 4Å: Chain E: F.101, F.105 Chain F: L.17, T.21, F.25, K.32, L.104, F.105 Chain G: K.32 Ligands: LHG.15, LHG.22, LHG.23, LHG.26 Ligand excluded by PLIP LHG.19: 9 residues within 4Å: Chain E: M.2, F.14, L.17, L.93 Chain F: M.1, M.2 Ligands: LHG.15, LHG.16, LHG.23 Ligand excluded by PLIP LHG.22: 12 residues within 4Å: Chain F: F.101, F.105 Chain G: L.17, T.21, F.25, K.32, L.104, F.105 Chain H: K.32 Ligands: LHG.18, LHG.25, LHG.26 Ligand excluded by PLIP LHG.23: 9 residues within 4Å: Chain F: M.2, F.14, L.17, L.93 Chain G: M.1, M.2 Ligands: LHG.18, LHG.19, LHG.26 Ligand excluded by PLIP LHG.25: 12 residues within 4Å: Chain G: F.101, F.105 Chain H: L.17, T.21, F.25, K.32, L.104, F.105 Chain I: K.32 Ligands: LHG.22, LHG.28, LHG.29 Ligand excluded by PLIP LHG.26: 10 residues within 4Å: Chain G: M.2, F.14, L.17, L.93 Chain H: M.1, M.2 Ligands: LHG.18, LHG.22, LHG.23, LHG.29 Ligand excluded by PLIP LHG.28: 12 residues within 4Å: Chain H: F.101, F.105 Chain I: L.17, T.21, F.25, K.32, L.104, F.105 Chain J: K.32 Ligands: LHG.3, LHG.25, LHG.32 Ligand excluded by PLIP LHG.29: 9 residues within 4Å: Chain H: M.2, F.14, L.17, L.93 Chain I: M.1, M.2 Ligands: LHG.25, LHG.26, LHG.32 Ligand excluded by PLIP LHG.31: 12 residues within 4Å: Chain A: K.32 Chain I: F.101, F.105 Chain J: L.17, T.21, F.25, K.32, L.104, F.105 Ligands: LHG.2, LHG.3, LHG.6 Ligand excluded by PLIP LHG.32: 9 residues within 4Å: Chain I: M.2, F.14, L.17, L.93 Chain J: M.1, M.2 Ligands: LHG.3, LHG.28, LHG.29 Ligand excluded by PLIP

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

UMQ.10: 5 residues within 4Å: Chain C: Q.54, P.125, E.126, T.129, I.132 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.132 Hydrogen bonds: C:Q.54 UMQ.20: 7 residues within 4Å: Chain F: Q.54, I.57, L.61, P.125, E.126, A.128, T.129 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:I.57, F:L.61 Hydrogen bonds: F:Q.54, F:T.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murata, T. et al., Crystal structure of Lithium bound rotor ring of the V-ATPase from Enterococcus hirae. To be Published

Release Date

2006-06-27

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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