SMTL ID : 4i1d.1

The crystal structure of an ABC transporter substrate-binding protein from Bradyrhizobium japonicum USDA 110

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-octamer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: P.178, T.181 Chain G: P.163, W.305 Ligand excluded by PLIP SO4.2: 2 residues within 4Å: Chain A: P.91, E.92 Ligand excluded by PLIP SO4.3: 2 residues within 4Å: Chain A: G.155, R.168 Ligand excluded by PLIP SO4.4: 4 residues within 4Å: Chain A: M.301, S.302, Y.303, A.304 Ligand excluded by PLIP SO4.5: 6 residues within 4Å: Chain A: K.47, R.69, Q.73 Ligands: SO4.8, ACT.12, SO4.23 Ligand excluded by PLIP SO4.6: 5 residues within 4Å: Chain A: S.210, K.214, I.265, D.266, R.284 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain A: N.122, T.222, K.297 Ligand excluded by PLIP SO4.8: 2 residues within 4Å: Chain A: K.47 Ligands: SO4.5 Ligand excluded by PLIP SO4.9: 2 residues within 4Å: Chain A: R.136 Chain G: A.304 Ligand excluded by PLIP SO4.18: 6 residues within 4Å: Chain B: S.210, A.211, K.214, I.265, D.266, R.284 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain B: P.63, Y.105, R.140 Ligand excluded by PLIP SO4.20: 2 residues within 4Å: Chain B: D.154, R.168 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain B: R.136 Chain H: A.304 Ligands: SO4.128 Ligand excluded by PLIP SO4.22: 4 residues within 4Å: Chain B: F.170, R.317, S.320, F.321 Ligand excluded by PLIP SO4.23: 6 residues within 4Å: Chain B: W.43, K.47, R.69, Q.73, E.312 Ligands: SO4.5 Ligand excluded by PLIP SO4.24: 2 residues within 4Å: Chain B: E.92, R.95 Ligand excluded by PLIP SO4.34: 5 residues within 4Å: Chain C: P.63, Y.105, R.140, I.144 Ligands: ACT.51 Ligand excluded by PLIP SO4.35: 5 residues within 4Å: Chain C: W.43, K.47, R.69, Q.73 Ligands: SO4.40 Ligand excluded by PLIP SO4.36: 8 residues within 4Å: Chain C: G.207, S.210, A.211, K.214, I.265, D.266, R.284 Ligands: SO4.42 Ligand excluded by PLIP SO4.37: 5 residues within 4Å: Chain C: F.170, E.174, R.317, F.321 Chain E: Q.323 Ligand excluded by PLIP SO4.38: 2 residues within 4Å: Chain C: V.156, R.168 Ligand excluded by PLIP SO4.39: 3 residues within 4Å: Chain A: A.45, T.48 Chain C: Q.189 Ligand excluded by PLIP SO4.40: 4 residues within 4Å: Chain C: R.69, P.309, E.312 Ligands: SO4.35 Ligand excluded by PLIP SO4.41: 2 residues within 4Å: Chain C: K.118, D.119 Ligand excluded by PLIP SO4.42: 4 residues within 4Å: Chain C: K.214, L.263, R.284 Ligands: SO4.36 Ligand excluded by PLIP SO4.56: 5 residues within 4Å: Chain D: P.163, W.305, S.308 Chain F: T.181 Ligands: SO4.93 Ligand excluded by PLIP SO4.57: 5 residues within 4Å: Chain D: P.63, Y.105, R.140, I.144 Ligands: GOL.68 Ligand excluded by PLIP SO4.58: 5 residues within 4Å: Chain D: W.43, K.47, R.69, Q.73, E.312 Ligand excluded by PLIP SO4.59: 2 residues within 4Å: Chain D: V.156, R.168 Ligand excluded by PLIP SO4.60: 2 residues within 4Å: Chain D: P.91, E.92 Ligand excluded by PLIP SO4.61: 6 residues within 4Å: Chain D: S.210, K.214, H.264, I.265, D.266, R.284 Ligand excluded by PLIP SO4.62: 4 residues within 4Å: Chain D: M.301, S.302, Y.303, A.304 Ligand excluded by PLIP SO4.63: 4 residues within 4Å: Chain D: F.170, E.174, R.317, F.321 Ligand excluded by PLIP SO4.64: 3 residues within 4Å: Chain D: P.178, H.179 Chain G: K.171 Ligand excluded by PLIP SO4.73: 4 residues within 4Å: Chain C: P.163, W.305 Chain E: P.178, T.181 Ligand excluded by PLIP SO4.74: 2 residues within 4Å: Chain E: P.91, E.92 Ligand excluded by PLIP SO4.75: 2 residues within 4Å: Chain E: G.155, R.168 Ligand excluded by PLIP SO4.76: 4 residues within 4Å: Chain E: M.301, S.302, Y.303, A.304 Ligand excluded by PLIP SO4.77: 6 residues within 4Å: Chain E: K.47, R.69, Q.73 Ligands: SO4.80, ACT.84, SO4.95 Ligand excluded by PLIP SO4.78: 5 residues within 4Å: Chain E: S.210, K.214, I.265, D.266, R.284 Ligand excluded by PLIP SO4.79: 3 residues within 4Å: Chain E: N.122, T.222, K.297 Ligand excluded by PLIP SO4.80: 2 residues within 4Å: Chain E: K.47 Ligands: SO4.77 Ligand excluded by PLIP SO4.81: 2 residues within 4Å: Chain C: A.304 Chain E: R.136 Ligand excluded by PLIP SO4.90: 6 residues within 4Å: Chain F: S.210, A.211, K.214, I.265, D.266, R.284 Ligand excluded by PLIP SO4.91: 3 residues within 4Å: Chain F: P.63, Y.105, R.140 Ligand excluded by PLIP SO4.92: 2 residues within 4Å: Chain F: D.154, R.168 Ligand excluded by PLIP SO4.93: 3 residues within 4Å: Chain D: A.304 Chain F: R.136 Ligands: SO4.56 Ligand excluded by PLIP SO4.94: 4 residues within 4Å: Chain F: F.170, R.317, S.320, F.321 Ligand excluded by PLIP SO4.95: 6 residues within 4Å: Chain F: W.43, K.47, R.69, Q.73, E.312 Ligands: SO4.77 Ligand excluded by PLIP SO4.96: 2 residues within 4Å: Chain F: E.92, R.95 Ligand excluded by PLIP SO4.106: 5 residues within 4Å: Chain G: P.63, Y.105, R.140, I.144 Ligands: ACT.123 Ligand excluded by PLIP SO4.107: 5 residues within 4Å: Chain G: W.43, K.47, R.69, Q.73 Ligands: SO4.112 Ligand excluded by PLIP SO4.108: 8 residues within 4Å: Chain G: G.207, S.210, A.211, K.214, I.265, D.266, R.284 Ligands: SO4.114 Ligand excluded by PLIP SO4.109: 5 residues within 4Å: Chain A: Q.323 Chain G: F.170, E.174, R.317, F.321 Ligand excluded by PLIP SO4.110: 2 residues within 4Å: Chain G: V.156, R.168 Ligand excluded by PLIP SO4.111: 3 residues within 4Å: Chain E: A.45, T.48 Chain G: Q.189 Ligand excluded by PLIP SO4.112: 4 residues within 4Å: Chain G: R.69, P.309, E.312 Ligands: SO4.107 Ligand excluded by PLIP SO4.113: 2 residues within 4Å: Chain G: K.118, D.119 Ligand excluded by PLIP SO4.114: 4 residues within 4Å: Chain G: K.214, L.263, R.284 Ligands: SO4.108 Ligand excluded by PLIP SO4.128: 5 residues within 4Å: Chain B: T.181 Chain H: P.163, W.305, S.308 Ligands: SO4.21 Ligand excluded by PLIP SO4.129: 5 residues within 4Å: Chain H: P.63, Y.105, R.140, I.144 Ligands: GOL.140 Ligand excluded by PLIP SO4.130: 5 residues within 4Å: Chain H: W.43, K.47, R.69, Q.73, E.312 Ligand excluded by PLIP SO4.131: 2 residues within 4Å: Chain H: V.156, R.168 Ligand excluded by PLIP SO4.132: 2 residues within 4Å: Chain H: P.91, E.92 Ligand excluded by PLIP SO4.133: 6 residues within 4Å: Chain H: S.210, K.214, H.264, I.265, D.266, R.284 Ligand excluded by PLIP SO4.134: 4 residues within 4Å: Chain H: M.301, S.302, Y.303, A.304 Ligand excluded by PLIP SO4.135: 4 residues within 4Å: Chain H: F.170, E.174, R.317, F.321 Ligand excluded by PLIP SO4.136: 3 residues within 4Å: Chain C: K.171 Chain H: P.178, H.179 Ligand excluded by PLIP

30 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 6 residues within 4Å: Chain A: P.63, Y.66, Y.105, R.140, H.142, W.205 Ligand excluded by PLIP GOL.25: 5 residues within 4Å: Chain B: N.122, T.222, Y.223, K.297 Ligands: ACT.31 Ligand excluded by PLIP GOL.26: 4 residues within 4Å: Chain B: M.301, S.302, Y.303, A.304 Ligand excluded by PLIP GOL.27: 6 residues within 4Å: Chain B: Q.10, Y.14, E.103, Y.105, T.231, Y.267 Ligand excluded by PLIP GOL.28: 9 residues within 4Å: Chain B: S.112, K.114, L.194, N.195, G.197, A.217, K.218 Chain D: K.54 Ligands: ACT.32 Ligand excluded by PLIP GOL.29: 4 residues within 4Å: Chain B: A.239, P.240, L.242, E.243 Ligand excluded by PLIP GOL.43: 5 residues within 4Å: Chain C: N.122, T.222, Y.223, K.297 Ligands: ACT.52 Ligand excluded by PLIP GOL.44: 2 residues within 4Å: Chain C: H.179 Chain H: K.171 Ligand excluded by PLIP GOL.45: 4 residues within 4Å: Chain C: M.301, S.302, Y.303, A.304 Ligand excluded by PLIP GOL.46: 7 residues within 4Å: Chain C: Q.10, Y.14, E.103, Y.105, W.205, Y.267 Ligands: MLT.55 Ligand excluded by PLIP GOL.47: 5 residues within 4Å: Chain C: Y.94, F.104, L.228, S.290, A.295 Ligand excluded by PLIP GOL.65: 5 residues within 4Å: Chain D: N.122, T.222, Y.223, K.297 Ligands: ACT.70 Ligand excluded by PLIP GOL.66: 6 residues within 4Å: Chain D: Q.10, Y.14, E.103, Y.105, W.205, Y.267 Ligand excluded by PLIP GOL.67: 6 residues within 4Å: Chain D: T.64, A.93, Y.94, R.95, S.101, Y.303 Ligand excluded by PLIP GOL.68: 7 residues within 4Å: Chain D: P.63, G.65, Y.66, I.144, Y.303, W.306 Ligands: SO4.57 Ligand excluded by PLIP GOL.82: 6 residues within 4Å: Chain E: P.63, Y.66, Y.105, R.140, H.142, W.205 Ligand excluded by PLIP GOL.97: 5 residues within 4Å: Chain F: N.122, T.222, Y.223, K.297 Ligands: ACT.103 Ligand excluded by PLIP GOL.98: 4 residues within 4Å: Chain F: M.301, S.302, Y.303, A.304 Ligand excluded by PLIP GOL.99: 6 residues within 4Å: Chain F: Q.10, Y.14, E.103, Y.105, T.231, Y.267 Ligand excluded by PLIP GOL.100: 9 residues within 4Å: Chain F: S.112, K.114, L.194, N.195, G.197, A.217, K.218 Chain H: K.54 Ligands: ACT.104 Ligand excluded by PLIP GOL.101: 4 residues within 4Å: Chain F: A.239, P.240, L.242, E.243 Ligand excluded by PLIP GOL.115: 5 residues within 4Å: Chain G: N.122, T.222, Y.223, K.297 Ligands: ACT.124 Ligand excluded by PLIP GOL.116: 2 residues within 4Å: Chain D: K.171 Chain G: H.179 Ligand excluded by PLIP GOL.117: 4 residues within 4Å: Chain G: M.301, S.302, Y.303, A.304 Ligand excluded by PLIP GOL.118: 7 residues within 4Å: Chain G: Q.10, Y.14, E.103, Y.105, W.205, Y.267 Ligands: MLT.127 Ligand excluded by PLIP GOL.119: 5 residues within 4Å: Chain G: Y.94, F.104, L.228, S.290, A.295 Ligand excluded by PLIP GOL.137: 5 residues within 4Å: Chain H: N.122, T.222, Y.223, K.297 Ligands: ACT.142 Ligand excluded by PLIP GOL.138: 6 residues within 4Å: Chain H: Q.10, Y.14, E.103, Y.105, W.205, Y.267 Ligand excluded by PLIP GOL.139: 6 residues within 4Å: Chain H: T.64, A.93, Y.94, R.95, S.101, Y.303 Ligand excluded by PLIP GOL.140: 7 residues within 4Å: Chain H: P.63, G.65, Y.66, I.144, Y.303, W.306 Ligands: SO4.129 Ligand excluded by PLIP

38 x ACT: ACETATE ION(Non-functional Binders)

ACT.11: 3 residues within 4Å: Chain A: Y.14, Y.105, Y.267 Ligand excluded by PLIP ACT.12: 8 residues within 4Å: Chain A: W.43, K.47, Y.66, R.69, G.70, Q.73, L.75 Ligands: SO4.5 Ligand excluded by PLIP ACT.13: 6 residues within 4Å: Chain A: P.63, G.65, Y.66, R.69, Y.303, W.306 Ligand excluded by PLIP ACT.14: 5 residues within 4Å: Chain A: S.112, K.114, L.194, N.195, K.218 Ligand excluded by PLIP ACT.15: 3 residues within 4Å: Chain A: F.170, R.317, F.321 Ligand excluded by PLIP ACT.16: 2 residues within 4Å: Chain A: F.221, Y.223 Ligand excluded by PLIP ACT.30: 2 residues within 4Å: Chain B: A.45, T.48 Ligand excluded by PLIP ACT.31: 2 residues within 4Å: Chain B: F.221 Ligands: GOL.25 Ligand excluded by PLIP ACT.32: 3 residues within 4Å: Chain B: N.195 Chain D: K.54 Ligands: GOL.28 Ligand excluded by PLIP ACT.48: 6 residues within 4Å: Chain A: Q.10, S.38, I.39 Chain C: Q.10, I.39, P.40 Ligand excluded by PLIP ACT.49: 4 residues within 4Å: Chain C: W.43, Y.66, E.312, E.315 Ligand excluded by PLIP ACT.50: 4 residues within 4Å: Chain C: V.50, G.74 Chain G: Q.73 Ligands: ACT.122 Ligand excluded by PLIP ACT.51: 6 residues within 4Å: Chain C: P.63, G.65, Y.66, I.144, Y.303 Ligands: SO4.34 Ligand excluded by PLIP ACT.52: 2 residues within 4Å: Chain C: F.221 Ligands: GOL.43 Ligand excluded by PLIP ACT.53: 3 residues within 4Å: Chain C: Y.111, Q.113, S.220 Ligand excluded by PLIP ACT.54: 4 residues within 4Å: Chain C: P.240, N.241, L.242, E.243 Ligand excluded by PLIP ACT.69: 6 residues within 4Å: Chain B: K.54 Chain D: S.112, K.114, L.194, N.195, K.218 Ligand excluded by PLIP ACT.70: 4 residues within 4Å: Chain D: F.221, Y.223, Q.287 Ligands: GOL.65 Ligand excluded by PLIP ACT.71: 5 residues within 4Å: Chain B: S.38 Chain D: Q.10, S.38, I.39, P.40 Ligand excluded by PLIP ACT.83: 3 residues within 4Å: Chain E: Y.14, Y.105, Y.267 Ligand excluded by PLIP ACT.84: 8 residues within 4Å: Chain E: W.43, K.47, Y.66, R.69, G.70, Q.73, L.75 Ligands: SO4.77 Ligand excluded by PLIP ACT.85: 6 residues within 4Å: Chain E: P.63, G.65, Y.66, R.69, Y.303, W.306 Ligand excluded by PLIP ACT.86: 5 residues within 4Å: Chain E: S.112, K.114, L.194, N.195, K.218 Ligand excluded by PLIP ACT.87: 3 residues within 4Å: Chain E: F.170, R.317, F.321 Ligand excluded by PLIP ACT.88: 2 residues within 4Å: Chain E: F.221, Y.223 Ligand excluded by PLIP ACT.102: 2 residues within 4Å: Chain F: A.45, T.48 Ligand excluded by PLIP ACT.103: 2 residues within 4Å: Chain F: F.221 Ligands: GOL.97 Ligand excluded by PLIP ACT.104: 3 residues within 4Å: Chain F: N.195 Chain H: K.54 Ligands: GOL.100 Ligand excluded by PLIP ACT.120: 6 residues within 4Å: Chain E: Q.10, S.38, I.39 Chain G: Q.10, I.39, P.40 Ligand excluded by PLIP ACT.121: 4 residues within 4Å: Chain G: W.43, Y.66, E.312, E.315 Ligand excluded by PLIP ACT.122: 4 residues within 4Å: Chain C: Q.73 Chain G: V.50, G.74 Ligands: ACT.50 Ligand excluded by PLIP ACT.123: 6 residues within 4Å: Chain G: P.63, G.65, Y.66, I.144, Y.303 Ligands: SO4.106 Ligand excluded by PLIP ACT.124: 2 residues within 4Å: Chain G: F.221 Ligands: GOL.115 Ligand excluded by PLIP ACT.125: 3 residues within 4Å: Chain G: Y.111, Q.113, S.220 Ligand excluded by PLIP ACT.126: 4 residues within 4Å: Chain G: P.240, N.241, L.242, E.243 Ligand excluded by PLIP ACT.141: 6 residues within 4Å: Chain F: K.54 Chain H: S.112, K.114, L.194, N.195, K.218 Ligand excluded by PLIP ACT.142: 4 residues within 4Å: Chain H: F.221, Y.223, Q.287 Ligands: GOL.137 Ligand excluded by PLIP ACT.143: 5 residues within 4Å: Chain F: S.38 Chain H: Q.10, S.38, I.39, P.40 Ligand excluded by PLIP

8 x MLT: D-MALATE(Non-covalent)

MLT.17: 5 residues within 4Å: Chain A: T.185, S.186, G.187, W.205, R.208 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.205 Hydrogen bonds: A:G.187, A:A.188, A:R.208 Salt bridges: A:R.208 MLT.33: 6 residues within 4Å: Chain B: T.185, S.186, G.187, A.188, W.205, R.208 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.205 Hydrogen bonds: B:G.187, B:A.188, B:R.208 Salt bridges: B:R.208 MLT.55: 7 residues within 4Å: Chain C: T.185, S.186, G.187, A.188, W.205, R.208 Ligands: GOL.46 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:W.205 Hydrogen bonds: C:G.187, C:A.188, C:R.208 Salt bridges: C:R.208 MLT.72: 6 residues within 4Å: Chain D: T.185, S.186, G.187, A.188, W.205, R.208 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:W.205 Hydrogen bonds: D:T.185, D:G.187, D:A.188, D:R.208 Salt bridges: D:R.208 MLT.89: 5 residues within 4Å: Chain E: T.185, S.186, G.187, W.205, R.208 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:W.205 Hydrogen bonds: E:G.187, E:A.188, E:R.208 Salt bridges: E:R.208 MLT.105: 6 residues within 4Å: Chain F: T.185, S.186, G.187, A.188, W.205, R.208 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:W.205 Hydrogen bonds: F:G.187, F:A.188, F:R.208 Salt bridges: F:R.208 MLT.127: 7 residues within 4Å: Chain G: T.185, S.186, G.187, A.188, W.205, R.208 Ligands: GOL.118 5 PLIP interactions: 5 interactions with chain G Hydrophobic interactions: G:W.205 Hydrogen bonds: G:G.187, G:A.188, G:R.208 Salt bridges: G:R.208 MLT.144: 6 residues within 4Å: Chain H: T.185, S.186, G.187, A.188, W.205, R.208 6 PLIP interactions: 6 interactions with chain H Hydrophobic interactions: H:W.205 Hydrogen bonds: H:T.185, H:G.187, H:A.188, H:R.208 Salt bridges: H:R.208

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tan, K. et al., Structural and functional characterization of solute binding proteins for aromatic compounds derived from lignin: p-Coumaric acid and related aromatic acids. Proteins (2013)

Release Date

2012-12-05

Peptides

ABC transporter substrate-binding protein: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

ABC transporter substrate-binding protein