SMTL ID : 3pei.1

Crystal Structure of Cytosol Aminopeptidase from Francisella tularensis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-hexamer

Ligands

18 x K: POTASSIUM ION(Non-covalent)

K.1: 3 residues within 4Å: Chain A: T.194, Y.197, F.200 Ligand excluded by PLIP K.6: 1 residues within 4Å: Chain A: I.367 Ligand excluded by PLIP K.8: 5 residues within 4Å: Chain A: Q.207, G.222, S.225, M.227, S.228 Ligand excluded by PLIP K.25: 3 residues within 4Å: Chain B: T.194, Y.197, F.200 Ligand excluded by PLIP K.30: 1 residues within 4Å: Chain B: I.367 Ligand excluded by PLIP K.32: 5 residues within 4Å: Chain B: Q.207, G.222, S.225, M.227, S.228 Ligand excluded by PLIP K.49: 3 residues within 4Å: Chain C: T.194, Y.197, F.200 Ligand excluded by PLIP K.54: 1 residues within 4Å: Chain C: I.367 Ligand excluded by PLIP K.56: 5 residues within 4Å: Chain C: Q.207, G.222, S.225, M.227, S.228 Ligand excluded by PLIP K.73: 3 residues within 4Å: Chain D: T.194, Y.197, F.200 Ligand excluded by PLIP K.78: 1 residues within 4Å: Chain D: I.367 Ligand excluded by PLIP K.80: 5 residues within 4Å: Chain D: Q.207, G.222, S.225, M.227, S.228 Ligand excluded by PLIP K.97: 3 residues within 4Å: Chain E: T.194, Y.197, F.200 Ligand excluded by PLIP K.102: 1 residues within 4Å: Chain E: I.367 Ligand excluded by PLIP K.104: 5 residues within 4Å: Chain E: Q.207, G.222, S.225, M.227, S.228 Ligand excluded by PLIP K.121: 3 residues within 4Å: Chain F: T.194, Y.197, F.200 Ligand excluded by PLIP K.126: 1 residues within 4Å: Chain F: I.367 Ligand excluded by PLIP K.128: 5 residues within 4Å: Chain F: Q.207, G.222, S.225, M.227, S.228 Ligand excluded by PLIP

60 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 6 residues within 4Å: Chain A: D.155, K.158, I.159, L.291, L.293 Ligands: CL.5 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: P.406, Y.407, K.409, K.410 Chain F: K.80, D.371 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: K.353, K.382, L.383, S.386, E.444, Y.474, Q.478 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: Q.174, N.175, D.274, M.455 Ligand excluded by PLIP EDO.14: 7 residues within 4Å: Chain A: D.371, G.452, S.453, M.455, G.456, S.464, R.466 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain A: P.406, K.409 Chain F: I.74, E.77 Ligand excluded by PLIP EDO.17: 8 residues within 4Å: Chain A: M.2, I.122, T.125, Y.126, S.139, L.140, N.168 Ligands: CL.15 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain A: Q.389, A.390, A.393, H.473, S.477 Ligand excluded by PLIP EDO.21: 2 residues within 4Å: Chain A: V.318 Chain C: I.180 Ligand excluded by PLIP EDO.22: 7 residues within 4Å: Chain A: P.54, Q.88, K.91 Chain E: P.54, Q.88, K.91 Ligands: EDO.118 Ligand excluded by PLIP EDO.26: 6 residues within 4Å: Chain B: D.155, K.158, I.159, L.291, L.293 Ligands: CL.29 Ligand excluded by PLIP EDO.28: 6 residues within 4Å: Chain B: P.406, Y.407, K.409, K.410 Chain E: K.80, D.371 Ligand excluded by PLIP EDO.36: 7 residues within 4Å: Chain B: K.353, K.382, L.383, S.386, E.444, Y.474, Q.478 Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain B: Q.174, N.175, D.274, M.455 Ligand excluded by PLIP EDO.38: 7 residues within 4Å: Chain B: D.371, G.452, S.453, M.455, G.456, S.464, R.466 Ligand excluded by PLIP EDO.40: 4 residues within 4Å: Chain B: P.406, K.409 Chain E: I.74, E.77 Ligand excluded by PLIP EDO.41: 8 residues within 4Å: Chain B: M.2, I.122, T.125, Y.126, S.139, L.140, N.168 Ligands: CL.39 Ligand excluded by PLIP EDO.44: 5 residues within 4Å: Chain B: Q.389, A.390, A.393, H.473, S.477 Ligand excluded by PLIP EDO.45: 2 residues within 4Å: Chain A: I.180 Chain B: V.318 Ligand excluded by PLIP EDO.46: 7 residues within 4Å: Chain B: P.54, Q.88, K.91 Chain D: P.54, Q.88, K.91 Ligands: EDO.94 Ligand excluded by PLIP EDO.50: 6 residues within 4Å: Chain C: D.155, K.158, I.159, L.291, L.293 Ligands: CL.53 Ligand excluded by PLIP EDO.52: 6 residues within 4Å: Chain C: P.406, Y.407, K.409, K.410 Chain D: K.80, D.371 Ligand excluded by PLIP EDO.60: 7 residues within 4Å: Chain C: K.353, K.382, L.383, S.386, E.444, Y.474, Q.478 Ligand excluded by PLIP EDO.61: 4 residues within 4Å: Chain C: Q.174, N.175, D.274, M.455 Ligand excluded by PLIP EDO.62: 7 residues within 4Å: Chain C: D.371, G.452, S.453, M.455, G.456, S.464, R.466 Ligand excluded by PLIP EDO.64: 4 residues within 4Å: Chain C: P.406, K.409 Chain D: I.74, E.77 Ligand excluded by PLIP EDO.65: 8 residues within 4Å: Chain C: M.2, I.122, T.125, Y.126, S.139, L.140, N.168 Ligands: CL.63 Ligand excluded by PLIP EDO.68: 5 residues within 4Å: Chain C: Q.389, A.390, A.393, H.473, S.477 Ligand excluded by PLIP EDO.69: 2 residues within 4Å: Chain B: I.180 Chain C: V.318 Ligand excluded by PLIP EDO.70: 7 residues within 4Å: Chain C: P.54, Q.88, K.91 Chain F: P.54, Q.88, K.91 Ligands: EDO.142 Ligand excluded by PLIP EDO.74: 6 residues within 4Å: Chain D: D.155, K.158, I.159, L.291, L.293 Ligands: CL.77 Ligand excluded by PLIP EDO.76: 6 residues within 4Å: Chain C: K.80, D.371 Chain D: P.406, Y.407, K.409, K.410 Ligand excluded by PLIP EDO.84: 7 residues within 4Å: Chain D: K.353, K.382, L.383, S.386, E.444, Y.474, Q.478 Ligand excluded by PLIP EDO.85: 4 residues within 4Å: Chain D: Q.174, N.175, D.274, M.455 Ligand excluded by PLIP EDO.86: 7 residues within 4Å: Chain D: D.371, G.452, S.453, M.455, G.456, S.464, R.466 Ligand excluded by PLIP EDO.88: 4 residues within 4Å: Chain C: I.74, E.77 Chain D: P.406, K.409 Ligand excluded by PLIP EDO.89: 8 residues within 4Å: Chain D: M.2, I.122, T.125, Y.126, S.139, L.140, N.168 Ligands: CL.87 Ligand excluded by PLIP EDO.92: 5 residues within 4Å: Chain D: Q.389, A.390, A.393, H.473, S.477 Ligand excluded by PLIP EDO.93: 2 residues within 4Å: Chain D: V.318 Chain F: I.180 Ligand excluded by PLIP EDO.94: 7 residues within 4Å: Chain B: P.54, Q.88, K.91 Chain D: P.54, Q.88, K.91 Ligands: EDO.46 Ligand excluded by PLIP EDO.98: 6 residues within 4Å: Chain E: D.155, K.158, I.159, L.291, L.293 Ligands: CL.101 Ligand excluded by PLIP EDO.100: 6 residues within 4Å: Chain B: K.80, D.371 Chain E: P.406, Y.407, K.409, K.410 Ligand excluded by PLIP EDO.108: 7 residues within 4Å: Chain E: K.353, K.382, L.383, S.386, E.444, Y.474, Q.478 Ligand excluded by PLIP EDO.109: 4 residues within 4Å: Chain E: Q.174, N.175, D.274, M.455 Ligand excluded by PLIP EDO.110: 7 residues within 4Å: Chain E: D.371, G.452, S.453, M.455, G.456, S.464, R.466 Ligand excluded by PLIP EDO.112: 4 residues within 4Å: Chain B: I.74, E.77 Chain E: P.406, K.409 Ligand excluded by PLIP EDO.113: 8 residues within 4Å: Chain E: M.2, I.122, T.125, Y.126, S.139, L.140, N.168 Ligands: CL.111 Ligand excluded by PLIP EDO.116: 5 residues within 4Å: Chain E: Q.389, A.390, A.393, H.473, S.477 Ligand excluded by PLIP EDO.117: 2 residues within 4Å: Chain D: I.180 Chain E: V.318 Ligand excluded by PLIP EDO.118: 7 residues within 4Å: Chain A: P.54, Q.88, K.91 Chain E: P.54, Q.88, K.91 Ligands: EDO.22 Ligand excluded by PLIP EDO.122: 6 residues within 4Å: Chain F: D.155, K.158, I.159, L.291, L.293 Ligands: CL.125 Ligand excluded by PLIP EDO.124: 6 residues within 4Å: Chain A: K.80, D.371 Chain F: P.406, Y.407, K.409, K.410 Ligand excluded by PLIP EDO.132: 7 residues within 4Å: Chain F: K.353, K.382, L.383, S.386, E.444, Y.474, Q.478 Ligand excluded by PLIP EDO.133: 4 residues within 4Å: Chain F: Q.174, N.175, D.274, M.455 Ligand excluded by PLIP EDO.134: 7 residues within 4Å: Chain F: D.371, G.452, S.453, M.455, G.456, S.464, R.466 Ligand excluded by PLIP EDO.136: 4 residues within 4Å: Chain A: I.74, E.77 Chain F: P.406, K.409 Ligand excluded by PLIP EDO.137: 8 residues within 4Å: Chain F: M.2, I.122, T.125, Y.126, S.139, L.140, N.168 Ligands: CL.135 Ligand excluded by PLIP EDO.140: 5 residues within 4Å: Chain F: Q.389, A.390, A.393, H.473, S.477 Ligand excluded by PLIP EDO.141: 2 residues within 4Å: Chain E: I.180 Chain F: V.318 Ligand excluded by PLIP EDO.142: 7 residues within 4Å: Chain C: P.54, Q.88, K.91 Chain F: P.54, Q.88, K.91 Ligands: EDO.70 Ligand excluded by PLIP

12 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 4 residues within 4Å: Chain A: N.23, K.26, D.102, E.106 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.23, A:K.26 Water bridges: A:Q.30 PEG.18: 7 residues within 4Å: Chain A: A.211, G.214, M.215, G.216, L.219, A.220, R.223 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.211, A:R.223 PEG.27: 4 residues within 4Å: Chain B: N.23, K.26, D.102, E.106 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.23, B:K.26 Water bridges: B:Q.30 PEG.42: 7 residues within 4Å: Chain B: A.211, G.214, M.215, G.216, L.219, A.220, R.223 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.211, B:R.223 PEG.51: 4 residues within 4Å: Chain C: N.23, K.26, D.102, E.106 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.23, C:K.26 Water bridges: C:Q.30 PEG.66: 7 residues within 4Å: Chain C: A.211, G.214, M.215, G.216, L.219, A.220, R.223 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.211, C:R.223 PEG.75: 4 residues within 4Å: Chain D: N.23, K.26, D.102, E.106 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.23, D:K.26 Water bridges: D:Q.30 PEG.90: 7 residues within 4Å: Chain D: A.211, G.214, M.215, G.216, L.219, A.220, R.223 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.211, D:R.223 PEG.99: 4 residues within 4Å: Chain E: N.23, K.26, D.102, E.106 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.23, E:K.26 Water bridges: E:Q.30 PEG.114: 7 residues within 4Å: Chain E: A.211, G.214, M.215, G.216, L.219, A.220, R.223 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:A.211, E:R.223 PEG.123: 4 residues within 4Å: Chain F: N.23, K.26, D.102, E.106 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:N.23, F:K.26 Water bridges: F:Q.30 PEG.138: 7 residues within 4Å: Chain F: A.211, G.214, M.215, G.216, L.219, A.220, R.223 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:A.211, F:R.223

30 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 1 residues within 4Å: Ligands: EDO.2 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: A.334, G.336, R.337, L.361 Ligand excluded by PLIP CL.9: 1 residues within 4Å: Chain A: D.442 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain A: N.168 Ligands: EDO.17 Ligand excluded by PLIP CL.24: 1 residues within 4Å: Chain A: G.428 Ligand excluded by PLIP CL.29: 1 residues within 4Å: Ligands: EDO.26 Ligand excluded by PLIP CL.31: 4 residues within 4Å: Chain B: A.334, G.336, R.337, L.361 Ligand excluded by PLIP CL.33: 1 residues within 4Å: Chain B: D.442 Ligand excluded by PLIP CL.39: 2 residues within 4Å: Chain B: N.168 Ligands: EDO.41 Ligand excluded by PLIP CL.48: 1 residues within 4Å: Chain B: G.428 Ligand excluded by PLIP CL.53: 1 residues within 4Å: Ligands: EDO.50 Ligand excluded by PLIP CL.55: 4 residues within 4Å: Chain C: A.334, G.336, R.337, L.361 Ligand excluded by PLIP CL.57: 1 residues within 4Å: Chain C: D.442 Ligand excluded by PLIP CL.63: 2 residues within 4Å: Chain C: N.168 Ligands: EDO.65 Ligand excluded by PLIP CL.72: 1 residues within 4Å: Chain C: G.428 Ligand excluded by PLIP CL.77: 1 residues within 4Å: Ligands: EDO.74 Ligand excluded by PLIP CL.79: 4 residues within 4Å: Chain D: A.334, G.336, R.337, L.361 Ligand excluded by PLIP CL.81: 1 residues within 4Å: Chain D: D.442 Ligand excluded by PLIP CL.87: 2 residues within 4Å: Chain D: N.168 Ligands: EDO.89 Ligand excluded by PLIP CL.96: 1 residues within 4Å: Chain D: G.428 Ligand excluded by PLIP CL.101: 1 residues within 4Å: Ligands: EDO.98 Ligand excluded by PLIP CL.103: 4 residues within 4Å: Chain E: A.334, G.336, R.337, L.361 Ligand excluded by PLIP CL.105: 1 residues within 4Å: Chain E: D.442 Ligand excluded by PLIP CL.111: 2 residues within 4Å: Chain E: N.168 Ligands: EDO.113 Ligand excluded by PLIP CL.120: 1 residues within 4Å: Chain E: G.428 Ligand excluded by PLIP CL.125: 1 residues within 4Å: Ligands: EDO.122 Ligand excluded by PLIP CL.127: 4 residues within 4Å: Chain F: A.334, G.336, R.337, L.361 Ligand excluded by PLIP CL.129: 1 residues within 4Å: Chain F: D.442 Ligand excluded by PLIP CL.135: 2 residues within 4Å: Chain F: N.168 Ligands: EDO.137 Ligand excluded by PLIP CL.144: 1 residues within 4Å: Chain F: G.428 Ligand excluded by PLIP

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

FMT.10: 5 residues within 4Å: Chain A: E.22, N.23, R.70, F.105, E.106 Ligand excluded by PLIP FMT.11: 6 residues within 4Å: Chain A: R.119, S.394, N.395, D.396, R.466, P.469 Ligand excluded by PLIP FMT.19: 3 residues within 4Å: Chain A: L.408, I.411, E.412 Ligand excluded by PLIP FMT.34: 5 residues within 4Å: Chain B: E.22, N.23, R.70, F.105, E.106 Ligand excluded by PLIP FMT.35: 6 residues within 4Å: Chain B: R.119, S.394, N.395, D.396, R.466, P.469 Ligand excluded by PLIP FMT.43: 3 residues within 4Å: Chain B: L.408, I.411, E.412 Ligand excluded by PLIP FMT.58: 5 residues within 4Å: Chain C: E.22, N.23, R.70, F.105, E.106 Ligand excluded by PLIP FMT.59: 6 residues within 4Å: Chain C: R.119, S.394, N.395, D.396, R.466, P.469 Ligand excluded by PLIP FMT.67: 3 residues within 4Å: Chain C: L.408, I.411, E.412 Ligand excluded by PLIP FMT.82: 5 residues within 4Å: Chain D: E.22, N.23, R.70, F.105, E.106 Ligand excluded by PLIP FMT.83: 6 residues within 4Å: Chain D: R.119, S.394, N.395, D.396, R.466, P.469 Ligand excluded by PLIP FMT.91: 3 residues within 4Å: Chain D: L.408, I.411, E.412 Ligand excluded by PLIP FMT.106: 5 residues within 4Å: Chain E: E.22, N.23, R.70, F.105, E.106 Ligand excluded by PLIP FMT.107: 6 residues within 4Å: Chain E: R.119, S.394, N.395, D.396, R.466, P.469 Ligand excluded by PLIP FMT.115: 3 residues within 4Å: Chain E: L.408, I.411, E.412 Ligand excluded by PLIP FMT.130: 5 residues within 4Å: Chain F: E.22, N.23, R.70, F.105, E.106 Ligand excluded by PLIP FMT.131: 6 residues within 4Å: Chain F: R.119, S.394, N.395, D.396, R.466, P.469 Ligand excluded by PLIP FMT.139: 3 residues within 4Å: Chain F: L.408, I.411, E.412 Ligand excluded by PLIP

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

SO4.23: 6 residues within 4Å: Chain A: E.235, Y.236, K.237, P.245, N.296, V.298 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.236, A:V.297 Water bridges: A:K.237, A:D.243, A:N.296, A:N.296 Salt bridges: A:K.237 SO4.47: 6 residues within 4Å: Chain B: E.235, Y.236, K.237, P.245, N.296, V.298 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.236, B:V.297 Water bridges: B:K.237, B:D.243, B:N.296, B:N.296 Salt bridges: B:K.237 SO4.71: 6 residues within 4Å: Chain C: E.235, Y.236, K.237, P.245, N.296, V.298 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Y.236, C:V.297 Water bridges: C:K.237, C:D.243, C:N.296, C:N.296 Salt bridges: C:K.237 SO4.95: 6 residues within 4Å: Chain D: E.235, Y.236, K.237, P.245, N.296, V.298 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:Y.236, D:V.297 Water bridges: D:K.237, D:D.243, D:N.296, D:N.296 Salt bridges: D:K.237 SO4.119: 6 residues within 4Å: Chain E: E.235, Y.236, K.237, P.245, N.296, V.298 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:Y.236, E:V.297 Water bridges: E:K.237, E:D.243, E:N.296, E:N.296 Salt bridges: E:K.237 SO4.143: 6 residues within 4Å: Chain F: E.235, Y.236, K.237, P.245, N.296, V.298 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:Y.236, F:V.297 Water bridges: F:K.237, F:D.243, F:N.296, F:N.296 Salt bridges: F:K.237

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maltseva, N. et al., Crystal Structure of Cytosol Aminopeptidase from Francisella tularensis. To be Published

Release Date

2010-12-01

Peptides

Cytosol aminopeptidase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Cytosol aminopeptidase