SMTL ID : 6m96.1

ATP-bound conformation of the WzmWzt O antigen ABC transporter

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

hetero-2-2-mer

Ligands

64 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)(Non-functional Binders)

LDA.1: 3 residues within 4Å: Chain A: R.21, I.25 Chain B: F.164 Ligand excluded by PLIP LDA.12: 6 residues within 4Å: Chain B: Y.136, Y.138, L.139, L.214, L.220, L.224 Ligand excluded by PLIP LDA.13: 6 residues within 4Å: Chain B: L.46, W.181 Ligands: LDA.17, LDA.25, LDA.26, LDA.63 Ligand excluded by PLIP LDA.14: 8 residues within 4Å: Chain B: Y.201, Y.202, H.223, Y.225, S.226, G.229, F.230, A.233 Ligand excluded by PLIP LDA.15: 9 residues within 4Å: Chain B: F.43, A.59, Y.60, Y.63, L.129, V.217, N.218 Ligands: LDA.26, LDA.28 Ligand excluded by PLIP LDA.16: 2 residues within 4Å: Chain D: Q.177, W.181 Ligand excluded by PLIP LDA.17: 4 residues within 4Å: Chain B: L.46 Chain D: W.181 Ligands: LDA.13, LDA.59 Ligand excluded by PLIP LDA.18: 4 residues within 4Å: Chain B: V.22, L.23, W.26 Ligands: LDA.42 Ligand excluded by PLIP LDA.19: 3 residues within 4Å: Chain B: F.152, F.238, Y.242 Ligand excluded by PLIP LDA.20: 4 residues within 4Å: Chain B: I.6, R.98, E.100, Y.242 Ligand excluded by PLIP LDA.21: 3 residues within 4Å: Chain B: I.148 Ligands: LDA.22, LDA.38 Ligand excluded by PLIP LDA.22: 2 residues within 4Å: Chain B: F.238 Ligands: LDA.21 Ligand excluded by PLIP LDA.23: 7 residues within 4Å: Chain B: V.36, L.37, T.40, L.41, S.44, Y.58 Ligands: LDA.24 Ligand excluded by PLIP LDA.24: 6 residues within 4Å: Chain B: Y.58, S.61, I.62, S.65, I.124 Ligands: LDA.23 Ligand excluded by PLIP LDA.25: 4 residues within 4Å: Chain B: L.46, I.47 Ligands: LDA.13, LDA.26 Ligand excluded by PLIP LDA.26: 9 residues within 4Å: Chain B: T.188, D.190, I.191, Y.219 Ligands: LDA.13, LDA.15, LDA.25, LDA.28, LDA.86 Ligand excluded by PLIP LDA.27: 2 residues within 4Å: Chain B: Y.145, L.231 Ligand excluded by PLIP LDA.28: 7 residues within 4Å: Chain B: Y.39, I.42, L.46, Y.60, V.186 Ligands: LDA.15, LDA.26 Ligand excluded by PLIP LDA.29: 1 residues within 4Å: Ligands: LDA.30 Ligand excluded by PLIP LDA.30: 2 residues within 4Å: Chain B: V.237 Ligands: LDA.29 Ligand excluded by PLIP LDA.31: 2 residues within 4Å: Chain A: L.22 Chain D: V.22 Ligand excluded by PLIP LDA.32: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LDA.33: 2 residues within 4Å: Chain B: Y.202, P.204 Ligand excluded by PLIP LDA.34: 4 residues within 4Å: Chain B: F.179, L.199, Y.202 Ligands: LDA.35 Ligand excluded by PLIP LDA.35: 1 residues within 4Å: Ligands: LDA.34 Ligand excluded by PLIP LDA.36: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LDA.37: 3 residues within 4Å: Chain B: P.141, L.144 Ligands: LDA.38 Ligand excluded by PLIP LDA.38: 3 residues within 4Å: Chain B: L.144 Ligands: LDA.21, LDA.37 Ligand excluded by PLIP LDA.39: 4 residues within 4Å: Chain B: H.45 Chain D: P.193, F.195 Ligands: LDA.40 Ligand excluded by PLIP LDA.40: 5 residues within 4Å: Chain D: W.181, I.191, L.192 Ligands: LDA.39, LDA.72 Ligand excluded by PLIP LDA.41: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LDA.42: 3 residues within 4Å: Chain B: G.24, I.25 Ligands: LDA.18 Ligand excluded by PLIP LDA.47: 3 residues within 4Å: Chain C: R.21, I.25 Chain D: F.164 Ligand excluded by PLIP LDA.58: 6 residues within 4Å: Chain D: Y.136, Y.138, L.139, L.214, L.220, L.224 Ligand excluded by PLIP LDA.59: 6 residues within 4Å: Chain D: L.46, W.181 Ligands: LDA.17, LDA.63, LDA.71, LDA.72 Ligand excluded by PLIP LDA.60: 8 residues within 4Å: Chain D: Y.201, Y.202, H.223, Y.225, S.226, G.229, F.230, A.233 Ligand excluded by PLIP LDA.61: 9 residues within 4Å: Chain D: F.43, A.59, Y.60, Y.63, L.129, V.217, N.218 Ligands: LDA.72, LDA.74 Ligand excluded by PLIP LDA.62: 2 residues within 4Å: Chain B: Q.177, W.181 Ligand excluded by PLIP LDA.63: 4 residues within 4Å: Chain B: W.181 Chain D: L.46 Ligands: LDA.13, LDA.59 Ligand excluded by PLIP LDA.64: 4 residues within 4Å: Chain D: V.22, L.23, W.26 Ligands: LDA.88 Ligand excluded by PLIP LDA.65: 3 residues within 4Å: Chain D: F.152, F.238, Y.242 Ligand excluded by PLIP LDA.66: 4 residues within 4Å: Chain D: I.6, R.98, E.100, Y.242 Ligand excluded by PLIP LDA.67: 3 residues within 4Å: Chain D: I.148 Ligands: LDA.68, LDA.84 Ligand excluded by PLIP LDA.68: 2 residues within 4Å: Chain D: F.238 Ligands: LDA.67 Ligand excluded by PLIP LDA.69: 7 residues within 4Å: Chain D: V.36, L.37, T.40, L.41, S.44, Y.58 Ligands: LDA.70 Ligand excluded by PLIP LDA.70: 6 residues within 4Å: Chain D: Y.58, S.61, I.62, S.65, I.124 Ligands: LDA.69 Ligand excluded by PLIP LDA.71: 4 residues within 4Å: Chain D: L.46, I.47 Ligands: LDA.59, LDA.72 Ligand excluded by PLIP LDA.72: 9 residues within 4Å: Chain D: T.188, D.190, I.191, Y.219 Ligands: LDA.40, LDA.59, LDA.61, LDA.71, LDA.74 Ligand excluded by PLIP LDA.73: 2 residues within 4Å: Chain D: Y.145, L.231 Ligand excluded by PLIP LDA.74: 7 residues within 4Å: Chain D: Y.39, I.42, L.46, Y.60, V.186 Ligands: LDA.61, LDA.72 Ligand excluded by PLIP LDA.75: 1 residues within 4Å: Ligands: LDA.76 Ligand excluded by PLIP LDA.76: 2 residues within 4Å: Chain D: V.237 Ligands: LDA.75 Ligand excluded by PLIP LDA.77: 2 residues within 4Å: Chain B: V.22 Chain C: L.22 Ligand excluded by PLIP LDA.78: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LDA.79: 2 residues within 4Å: Chain D: Y.202, P.204 Ligand excluded by PLIP LDA.80: 4 residues within 4Å: Chain D: F.179, L.199, Y.202 Ligands: LDA.81 Ligand excluded by PLIP LDA.81: 1 residues within 4Å: Ligands: LDA.80 Ligand excluded by PLIP LDA.82: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LDA.83: 3 residues within 4Å: Chain D: P.141, L.144 Ligands: LDA.84 Ligand excluded by PLIP LDA.84: 3 residues within 4Å: Chain D: L.144 Ligands: LDA.67, LDA.83 Ligand excluded by PLIP LDA.85: 4 residues within 4Å: Chain B: P.193, F.195 Chain D: H.45 Ligands: LDA.86 Ligand excluded by PLIP LDA.86: 5 residues within 4Å: Chain B: W.181, I.191, L.192 Ligands: LDA.26, LDA.85 Ligand excluded by PLIP LDA.87: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LDA.88: 3 residues within 4Å: Chain D: G.24, I.25 Ligands: LDA.64 Ligand excluded by PLIP

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: F.95, N.96, Y.97, E.98 Chain B: F.90 Ligands: GOL.7 Ligand excluded by PLIP GOL.3: 9 residues within 4Å: Chain A: D.167, Q.168, L.170, A.171, F.197, V.198, S.199, D.201 Chain C: A.171 Ligand excluded by PLIP GOL.4: 6 residues within 4Å: Chain A: Y.14, E.33, E.34 Chain C: D.134, F.135, K.138 Ligand excluded by PLIP GOL.5: 6 residues within 4Å: Chain A: N.57 Chain C: E.131, L.132, M.147, R.150 Ligands: ATP.8 Ligand excluded by PLIP GOL.6: 5 residues within 4Å: Chain A: S.62, K.66 Chain C: K.141, Y.143 Ligands: ATP.8 Ligand excluded by PLIP GOL.7: 3 residues within 4Å: Chain A: Y.97 Ligands: GOL.2, GOL.53 Ligand excluded by PLIP GOL.43: 8 residues within 4Å: Chain A: N.96, L.99, V.107 Chain B: L.9, K.88, F.90, L.91, F.102 Ligand excluded by PLIP GOL.44: 1 residues within 4Å: Chain B: H.223 Ligand excluded by PLIP GOL.48: 6 residues within 4Å: Chain C: F.95, N.96, Y.97, E.98 Chain D: F.90 Ligands: GOL.53 Ligand excluded by PLIP GOL.49: 9 residues within 4Å: Chain A: A.171 Chain C: D.167, Q.168, L.170, A.171, F.197, V.198, S.199, D.201 Ligand excluded by PLIP GOL.50: 6 residues within 4Å: Chain A: D.134, F.135, K.138 Chain C: Y.14, E.33, E.34 Ligand excluded by PLIP GOL.51: 6 residues within 4Å: Chain A: E.131, L.132, M.147, R.150 Chain C: N.57 Ligands: ATP.54 Ligand excluded by PLIP GOL.52: 5 residues within 4Å: Chain A: K.141, Y.143 Chain C: S.62, K.66 Ligands: ATP.54 Ligand excluded by PLIP GOL.53: 3 residues within 4Å: Chain C: Y.97 Ligands: GOL.7, GOL.48 Ligand excluded by PLIP GOL.89: 8 residues within 4Å: Chain C: N.96, L.99, V.107 Chain D: L.9, K.88, F.90, L.91, F.102 Ligand excluded by PLIP GOL.90: 1 residues within 4Å: Chain D: H.223 Ligand excluded by PLIP

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.8: 23 residues within 4Å: Chain A: Y.12, Y.14, L.35, V.37, P.56, N.57, G.58, A.59, G.60, K.61, S.62, T.63, H.200 Chain B: D.254 Chain C: F.135, T.142, Y.143, S.144, S.145, G.146, M.147 Ligands: GOL.5, GOL.6 27 PLIP interactions: 6 interactions with chain C, 20 interactions with chain A, 1 interactions with chain B Hydrogen bonds: C:S.144, C:S.144, C:S.145, C:G.146, C:M.147, A:N.57, A:G.58, A:A.59, A:G.60, A:K.61, A:S.62, A:S.62, A:T.63, A:T.63, A:Q.168, A:H.200, B:D.254 Water bridges: C:S.145, A:G.58, A:S.62, A:S.62, A:K.66, A:H.200 Salt bridges: A:K.61, A:K.61 pi-Stacking: A:Y.12, A:Y.12 ATP.54: 23 residues within 4Å: Chain A: F.135, T.142, Y.143, S.144, S.145, G.146, M.147 Chain C: Y.12, Y.14, L.35, V.37, P.56, N.57, G.58, A.59, G.60, K.61, S.62, T.63, H.200 Chain D: D.254 Ligands: GOL.51, GOL.52 28 PLIP interactions: 21 interactions with chain C, 6 interactions with chain A, 1 interactions with chain D Hydrogen bonds: C:Y.14, C:N.57, C:G.58, C:A.59, C:G.60, C:K.61, C:S.62, C:S.62, C:T.63, C:Q.168, C:H.200, A:S.144, A:S.144, A:S.145, A:G.146, A:M.147, D:D.254 Water bridges: C:Y.12, C:G.58, C:S.62, C:S.62, C:K.66, C:H.200, A:V.172 Salt bridges: C:K.61, C:K.61 pi-Stacking: C:Y.12, C:Y.12

4 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.9: 7 residues within 4Å: Chain A: F.182, L.185, K.189, I.207, L.208, C.209, D.210 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.189 Water bridges: A:K.206, A:C.209 PG4.10: 3 residues within 4Å: Chain A: W.9, W.36, K.76 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.76 PG4.55: 7 residues within 4Å: Chain C: F.182, L.185, K.189, I.207, L.208, C.209, D.210 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.189 Water bridges: C:K.206, C:C.209 PG4.56: 3 residues within 4Å: Chain C: W.9, W.36, K.76 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.76

2 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)

PEE.11: 5 residues within 4Å: Chain A: K.11, K.13, H.32, E.34 Chain B: K.250 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain A Water bridges: B:K.250, B:K.250, B:K.250, B:D.251, A:K.11, A:K.13, A:K.13 Salt bridges: B:K.250, A:K.11, A:K.13 Hydrogen bonds: A:H.32 PEE.57: 5 residues within 4Å: Chain C: K.11, K.13, H.32, E.34 Chain D: K.250 11 PLIP interactions: 5 interactions with chain D, 6 interactions with chain C Water bridges: D:K.250, D:K.250, D:K.250, D:D.251, C:K.11, C:K.13, C:K.13 Salt bridges: D:K.250, C:K.11, C:K.13 Hydrogen bonds: C:H.32

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

SO4.45: 4 residues within 4Å: Chain B: H.53, E.54, N.55, T.56 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.55, B:N.55, B:T.56, B:T.56, B:T.56 Water bridges: B:H.53, B:E.54 Salt bridges: B:H.53 SO4.91: 4 residues within 4Å: Chain D: H.53, E.54, N.55, T.56 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:N.55, D:N.55, D:T.56, D:T.56 Water bridges: D:H.53, D:E.54 Salt bridges: D:H.53

2 x P4G: 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE(Non-covalent)

P4G.46: 5 residues within 4Å: Chain B: R.166, D.167, E.170 Chain D: R.17, W.27 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:W.27 Hydrogen bonds: B:R.166 P4G.92: 5 residues within 4Å: Chain B: R.17, W.27 Chain D: R.166, D.167, E.170 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:W.27 Hydrogen bonds: D:R.166

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Caffalette, C.A. et al., A lipid gating mechanism for the channel-forming O antigen ABC transporter. Nat Commun (2019)

Release Date

2019-03-06

Peptides

ABC transporter: AC
Transport permease protein: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Membrane

We predict this structure to be a membrane protein.
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ABC transporter

Transport permease protein

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