SMTL ID : 3klz.1

Pentameric formate channel with formate bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-pentamer

Ligands

14 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.1: 7 residues within 4Å: Chain A: L.176, W.179, W.272, L.275 Chain B: S.39, Q.43, T.84 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.84 Hydrophobic interactions: A:L.176 BOG.2: 9 residues within 4Å: Chain A: L.68, L.72, M.192, I.195 Chain B: L.69, L.72, I.195 Ligands: FMT.7, BOG.14 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.69, B:L.72, A:L.68 Hydrogen bonds: A:M.192, A:L.196 BOG.3: 8 residues within 4Å: Chain A: K.32, S.39, I.83, T.84 Chain E: I.172, W.179, F.268, L.275 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain E Hydrogen bonds: A:K.32, A:K.32, A:I.83, E:W.179 Hydrophobic interactions: E:I.172, E:F.268, E:F.268 BOG.13: 2 residues within 4Å: Chain B: F.160, L.259 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.160, B:F.160, B:L.259 Water bridges: B:F.160 BOG.14: 8 residues within 4Å: Chain B: L.69, L.72, M.192, I.195 Ligands: BOG.2, FMT.7, BOG.28, BOG.47 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.69, B:L.72 Water bridges: B:M.192, B:L.196 BOG.15: 6 residues within 4Å: Chain B: K.223, Y.224, L.244, N.245, F.246, V.247 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.224, B:N.245, B:F.246, B:F.246, B:V.247, B:V.247 BOG.16: 4 residues within 4Å: Chain B: V.128, Y.224, F.225, F.246 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.128, B:F.225, B:F.246 BOG.17: 9 residues within 4Å: Chain B: V.82, I.83, T.181, F.182, A.184, R.185, S.186, L.187, K.190 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.82, B:F.182, B:K.190 Hydrogen bonds: B:A.184, B:R.185, B:K.190 Water bridges: B:L.187 Salt bridges: B:K.190 BOG.18: 6 residues within 4Å: Chain B: H.157, A.242, D.243, N.245, N.248 Ligands: FMT.24 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.245, B:N.248 BOG.28: 10 residues within 4Å: Chain C: L.69, L.72, M.192, I.195, L.196 Chain D: L.69, L.72, I.195 Ligands: BOG.14, BOG.36 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:L.69, C:L.72, D:L.72 Hydrogen bonds: C:M.192 BOG.29: 6 residues within 4Å: Chain C: I.125, V.128, F.129, P.217, Y.224, F.246 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:I.125, C:V.128, C:F.129, C:P.217, C:F.246 Hydrogen bonds: C:F.246 BOG.36: 11 residues within 4Å: Chain D: L.68, L.69, L.72, M.192, L.196 Chain E: L.72, V.191, I.195 Ligands: FMT.7, BOG.28, BOG.47 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:L.68, D:L.69, D:L.72, E:L.72 Hydrogen bonds: D:M.192 BOG.44: 13 residues within 4Å: Chain E: V.81, V.82, G.86, E.87, L.88, T.90, S.91, S.92, V.93, L.96, V.178, V.269 Ligands: FMT.46 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:T.90, E:L.96, E:V.178, E:V.269 Hydrogen bonds: E:L.88, E:T.90, E:S.91 BOG.47: 10 residues within 4Å: Chain A: L.69, I.195 Chain E: L.68, L.69, L.72, M.192, L.196 Ligands: FMT.7, BOG.14, BOG.36 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:L.68, E:L.69, A:L.69 Hydrogen bonds: E:M.192

39 x FMT: FORMIC ACID(Non-functional Binders)

FMT.4: 3 residues within 4Å: Chain A: T.55, A.58, T.66 Ligand excluded by PLIP FMT.5: 7 residues within 4Å: Chain A: G.57, H.59, D.60, D.140 Chain E: M.61, P.62, Y.63 Ligand excluded by PLIP FMT.6: 6 residues within 4Å: Chain A: H.154, K.155, H.158, G.205, E.207 Ligands: FMT.12 Ligand excluded by PLIP FMT.7: 5 residues within 4Å: Chain D: M.192 Ligands: BOG.2, BOG.14, BOG.36, BOG.47 Ligand excluded by PLIP FMT.8: 3 residues within 4Å: Chain A: F.89, T.114, Y.117 Ligand excluded by PLIP FMT.9: 3 residues within 4Å: Chain A: E.139, D.140 Chain E: Y.63 Ligand excluded by PLIP FMT.10: 3 residues within 4Å: Chain A: R.185 Chain B: R.185, S.186 Ligand excluded by PLIP FMT.11: 1 residues within 4Å: Chain A: P.217 Ligand excluded by PLIP FMT.12: 5 residues within 4Å: Chain A: Y.51, K.155, V.202, G.205 Ligands: FMT.6 Ligand excluded by PLIP FMT.19: 6 residues within 4Å: Chain A: H.154, L.166, S.204, G.205 Chain B: Q.136, E.139 Ligand excluded by PLIP FMT.20: 6 residues within 4Å: Chain B: A.58, H.59, M.61, P.62, Y.63, T.66 Ligand excluded by PLIP FMT.21: 2 residues within 4Å: Chain A: T.159 Chain B: R.135 Ligand excluded by PLIP FMT.22: 3 residues within 4Å: Chain B: M.138, G.141, M.233 Ligand excluded by PLIP FMT.23: 5 residues within 4Å: Chain B: S.183, R.185 Chain C: S.186, L.187, K.190 Ligand excluded by PLIP FMT.24: 6 residues within 4Å: Chain B: A.239, Q.240, Y.241, A.242, D.243 Ligands: BOG.18 Ligand excluded by PLIP FMT.25: 2 residues within 4Å: Chain B: F.89, W.113 Ligand excluded by PLIP FMT.26: 5 residues within 4Å: Chain B: F.48, Y.51, K.155, V.202, G.205 Ligand excluded by PLIP FMT.27: 2 residues within 4Å: Chain B: F.164, A.165 Ligand excluded by PLIP FMT.30: 4 residues within 4Å: Chain B: T.159, L.161 Chain C: A.133, R.135 Ligand excluded by PLIP FMT.31: 3 residues within 4Å: Chain C: F.89, W.113, Y.117 Ligand excluded by PLIP FMT.32: 1 residues within 4Å: Chain C: F.129 Ligand excluded by PLIP FMT.33: 7 residues within 4Å: Chain C: R.185 Chain D: A.184, S.186, L.187, K.190 Ligands: FMT.38, FMT.41 Ligand excluded by PLIP FMT.34: 3 residues within 4Å: Chain C: K.223, Y.224, A.242 Ligand excluded by PLIP FMT.35: 3 residues within 4Å: Chain B: L.176 Chain C: S.39, Q.43 Ligand excluded by PLIP FMT.37: 7 residues within 4Å: Chain D: L.88, F.89, T.90, S.91, N.171, V.174, H.208 Ligand excluded by PLIP FMT.38: 4 residues within 4Å: Chain C: R.185 Chain D: L.187, K.190 Ligands: FMT.33 Ligand excluded by PLIP FMT.39: 5 residues within 4Å: Chain D: A.58, M.61, P.62, Y.63, T.66 Ligand excluded by PLIP FMT.40: 3 residues within 4Å: Chain D: T.159, F.160, L.161 Ligand excluded by PLIP FMT.41: 5 residues within 4Å: Chain D: T.181, F.182, A.184, K.190 Ligands: FMT.33 Ligand excluded by PLIP FMT.42: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP FMT.43: 1 residues within 4Å: Chain D: S.39 Ligand excluded by PLIP FMT.45: 6 residues within 4Å: Chain E: L.88, F.89, N.171, V.174, H.208 Ligands: FMT.46 Ligand excluded by PLIP FMT.46: 6 residues within 4Å: Chain E: L.88, F.89, T.90, N.171 Ligands: BOG.44, FMT.45 Ligand excluded by PLIP FMT.48: 3 residues within 4Å: Chain E: Q.153, H.154, H.157 Ligand excluded by PLIP FMT.49: 4 residues within 4Å: Chain E: I.151, H.154, K.155 Ligands: FMT.52 Ligand excluded by PLIP FMT.50: 2 residues within 4Å: Chain E: W.113, T.114 Ligand excluded by PLIP FMT.51: 4 residues within 4Å: Chain E: V.128, F.129, P.217, G.221 Ligand excluded by PLIP FMT.52: 4 residues within 4Å: Chain E: Y.51, V.202, G.205 Ligands: FMT.49 Ligand excluded by PLIP FMT.53: 3 residues within 4Å: Chain D: L.176 Chain E: S.39, Q.43 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Waight, A.B. et al., Structure and mechanism of a pentameric formate channel. Nat.Struct.Mol.Biol. (2010)

Release Date

2009-12-15

Peptides

Putative formate transporter 1: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Membrane

We predict this structure to be a membrane protein.
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Putative formate transporter 1

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