SMTL ID : 2vd3.1

The structure of histidine inhibited HisG from Methanobacterium thermoautotrophicum

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-hexamer

Ligands

6 x HIS: HISTIDINE(Non-covalent)

HIS.1: 13 residues within 4Å: Chain A: G.237, M.238, T.239, G.240, T.242, H.256, A.257, V.258 Chain E: M.220, L.221, N.222, D.278, L.280 10 PLIP interactions: 5 interactions with chain A, 3 interactions with chain E, 2 Ligand-Ligand interactions Hydrogen bonds: A:M.238, A:T.239, A:G.240, A:T.242, A:V.258, E:N.222, E:N.222, E:D.278, H.1 Salt bridges: H.1 HIS.15: 13 residues within 4Å: Chain B: G.237, M.238, T.239, G.240, T.242, H.256, A.257, V.258 Chain D: M.220, L.221, N.222, D.278, L.280 12 PLIP interactions: 6 interactions with chain B, 2 interactions with chain D, 4 Ligand-Ligand interactions Hydrogen bonds: B:M.238, B:T.239, B:G.240, B:T.242, B:T.242, B:V.258, D:N.222, D:D.278, H.15, H.15 Water bridges: H.15 Salt bridges: H.15 HIS.30: 13 residues within 4Å: Chain A: M.220, L.221, N.222, D.278, L.280 Chain C: G.237, M.238, T.239, G.240, T.242, H.256, A.257, V.258 10 PLIP interactions: 5 interactions with chain C, 3 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: C:M.238, C:T.239, C:G.240, C:T.242, C:V.258, A:N.222, A:N.222, A:D.278, H.30 Salt bridges: H.30 HIS.44: 13 residues within 4Å: Chain D: G.237, M.238, T.239, G.240, T.242, H.256, A.257, V.258 Chain F: M.220, L.221, N.222, D.278, L.280 12 PLIP interactions: 6 interactions with chain D, 4 Ligand-Ligand interactions, 2 interactions with chain F Hydrogen bonds: D:M.238, D:T.239, D:G.240, D:T.242, D:T.242, D:V.258, H.44, H.44, F:N.222, F:D.278 Water bridges: H.44 Salt bridges: H.44 HIS.59: 13 residues within 4Å: Chain C: M.220, L.221, N.222, D.278, L.280 Chain E: G.237, M.238, T.239, G.240, T.242, H.256, A.257, V.258 10 PLIP interactions: 5 interactions with chain E, 3 interactions with chain C, 2 Ligand-Ligand interactions Hydrogen bonds: E:M.238, E:T.239, E:G.240, E:T.242, E:V.258, C:N.222, C:N.222, C:D.278, H.59 Salt bridges: H.59 HIS.73: 13 residues within 4Å: Chain B: M.220, L.221, N.222, D.278, L.280 Chain F: G.237, M.238, T.239, G.240, T.242, H.256, A.257, V.258 12 PLIP interactions: 2 interactions with chain B, 4 Ligand-Ligand interactions, 6 interactions with chain F Hydrogen bonds: B:N.222, B:D.278, H.73, H.73, F:M.238, F:T.239, F:G.240, F:T.242, F:T.242, F:V.258 Water bridges: H.73 Salt bridges: H.73

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

CL.2: 1 residues within 4Å: Chain A: S.162 Ligand excluded by PLIP CL.5: 5 residues within 4Å: Chain A: P.3, K.196, S.197, G.198, I.199 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain A: K.185 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain A: L.96, E.121, F.122, T.159, D.160 Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain B: E.141 Ligand excluded by PLIP CL.19: 5 residues within 4Å: Chain B: T.120, E.121, F.122, T.146, T.159 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain B: P.3, K.196, G.198, I.199 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain B: L.173, R.174, V.175 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain B: A.54, A.55 Ligand excluded by PLIP CL.31: 1 residues within 4Å: Chain C: S.162 Ligand excluded by PLIP CL.34: 5 residues within 4Å: Chain C: P.3, K.196, S.197, G.198, I.199 Ligand excluded by PLIP CL.35: 1 residues within 4Å: Chain C: K.185 Ligand excluded by PLIP CL.36: 5 residues within 4Å: Chain C: L.96, E.121, F.122, T.159, D.160 Ligand excluded by PLIP CL.45: 1 residues within 4Å: Chain D: E.141 Ligand excluded by PLIP CL.48: 5 residues within 4Å: Chain D: T.120, E.121, F.122, T.146, T.159 Ligand excluded by PLIP CL.49: 4 residues within 4Å: Chain D: P.3, K.196, G.198, I.199 Ligand excluded by PLIP CL.50: 3 residues within 4Å: Chain D: L.173, R.174, V.175 Ligand excluded by PLIP CL.51: 2 residues within 4Å: Chain D: A.54, A.55 Ligand excluded by PLIP CL.60: 1 residues within 4Å: Chain E: S.162 Ligand excluded by PLIP CL.63: 5 residues within 4Å: Chain E: P.3, K.196, S.197, G.198, I.199 Ligand excluded by PLIP CL.64: 1 residues within 4Å: Chain E: K.185 Ligand excluded by PLIP CL.65: 5 residues within 4Å: Chain E: L.96, E.121, F.122, T.159, D.160 Ligand excluded by PLIP CL.74: 1 residues within 4Å: Chain F: E.141 Ligand excluded by PLIP CL.77: 5 residues within 4Å: Chain F: T.120, E.121, F.122, T.146, T.159 Ligand excluded by PLIP CL.78: 4 residues within 4Å: Chain F: P.3, K.196, G.198, I.199 Ligand excluded by PLIP CL.79: 3 residues within 4Å: Chain F: L.173, R.174, V.175 Ligand excluded by PLIP CL.80: 2 residues within 4Å: Chain F: A.54, A.55 Ligand excluded by PLIP

9 x IMD: IMIDAZOLE(Non-covalent)

IMD.3: 4 residues within 4Å: Chain A: E.127, D.136, A.137, E.138 No protein-ligand interaction detected (PLIP) IMD.4: 3 residues within 4Å: Chain A: H.44, E.202 Chain E: K.262 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.202 IMD.18: 1 residues within 4Å: Chain B: D.111 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.111 IMD.32: 4 residues within 4Å: Chain C: E.127, D.136, A.137, E.138 No protein-ligand interaction detected (PLIP) IMD.33: 3 residues within 4Å: Chain A: K.262 Chain C: H.44, E.202 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.202 IMD.47: 1 residues within 4Å: Chain D: D.111 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.111 IMD.61: 4 residues within 4Å: Chain E: E.127, D.136, A.137, E.138 No protein-ligand interaction detected (PLIP) IMD.62: 3 residues within 4Å: Chain C: K.262 Chain E: H.44, E.202 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.202 IMD.76: 1 residues within 4Å: Chain F: D.111 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:D.111

27 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 2 residues within 4Å: Chain A: D.160, L.161 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.160 MG.9: 1 residues within 4Å: Chain A: E.84 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.84 MG.10: 3 residues within 4Å: Chain A: E.24, G.29, Q.43 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.24 MG.11: 2 residues within 4Å: Chain A: D.177, T.178 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.177, A:D.177 MG.17: 2 residues within 4Å: Chain A: D.63 Chain B: E.138 No protein-ligand interaction detected (PLIP) MG.23: 5 residues within 4Å: Chain B: S.11, K.12, S.52, R.53, A.54 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:K.12 MG.24: 2 residues within 4Å: Chain B: E.147, D.160 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.147, B:D.160 MG.25: 4 residues within 4Å: Chain B: G.13, R.14, S.16, E.17 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:G.13 MG.26: 2 residues within 4Å: Chain B: S.11, R.53 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.11, H2O.2, H2O.2 MG.37: 2 residues within 4Å: Chain C: D.160, L.161 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.160 MG.38: 1 residues within 4Å: Chain C: E.84 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.84 MG.39: 3 residues within 4Å: Chain C: E.24, G.29, Q.43 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.24 MG.40: 2 residues within 4Å: Chain C: D.177, T.178 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.177, C:D.177 MG.46: 2 residues within 4Å: Chain C: D.63 Chain D: E.138 No protein-ligand interaction detected (PLIP) MG.52: 5 residues within 4Å: Chain D: S.11, K.12, S.52, R.53, A.54 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:K.12 MG.53: 2 residues within 4Å: Chain D: E.147, D.160 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.147, D:D.160 MG.54: 4 residues within 4Å: Chain D: G.13, R.14, S.16, E.17 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:G.13 MG.55: 2 residues within 4Å: Chain D: S.11, R.53 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:S.11, H2O.4, H2O.4 MG.66: 2 residues within 4Å: Chain E: D.160, L.161 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.160 MG.67: 1 residues within 4Å: Chain E: E.84 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.84 MG.68: 3 residues within 4Å: Chain E: E.24, G.29, Q.43 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.24 MG.69: 2 residues within 4Å: Chain E: D.177, T.178 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.177, E:D.177 MG.75: 2 residues within 4Å: Chain E: D.63 Chain F: E.138 No protein-ligand interaction detected (PLIP) MG.81: 5 residues within 4Å: Chain F: S.11, K.12, S.52, R.53, A.54 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:K.12 MG.82: 2 residues within 4Å: Chain F: E.147, D.160 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:E.147, F:D.160 MG.83: 4 residues within 4Å: Chain F: G.13, R.14, S.16, E.17 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:G.13 MG.84: 2 residues within 4Å: Chain F: S.11, R.53 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:S.11, H2O.6, H2O.6

15 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.12: 6 residues within 4Å: Chain A: E.121, F.122, E.141, L.142, T.143 Ligands: MPD.27 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.121, A:F.122 Hydrogen bonds: A:E.141, A:E.141 MPD.14: 6 residues within 4Å: Chain A: K.4, R.6, E.48, A.65, D.67, K.196 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.4, A:R.6 Hydrogen bonds: A:R.6, A:R.6 MPD.27: 5 residues within 4Å: Chain B: E.121, E.141, L.142, T.143 Ligands: MPD.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.121, B:L.142 MPD.28: 7 residues within 4Å: Chain B: K.4, I.5, R.6, G.64, A.65, D.67, K.196 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:K.4 Hydrogen bonds: B:K.4, B:R.6, B:K.196, B:K.196 MPD.29: 5 residues within 4Å: Chain B: S.95, S.162, S.163, G.165, V.175 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.175 MPD.41: 6 residues within 4Å: Chain C: E.121, F.122, E.141, L.142, T.143 Ligands: MPD.56 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:E.121, C:F.122 Hydrogen bonds: C:E.141, C:E.141 MPD.43: 6 residues within 4Å: Chain C: K.4, R.6, E.48, A.65, D.67, K.196 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:K.4, C:R.6 Hydrogen bonds: C:R.6, C:R.6 MPD.56: 5 residues within 4Å: Chain D: E.121, E.141, L.142, T.143 Ligands: MPD.41 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.121, D:L.142 MPD.57: 7 residues within 4Å: Chain D: K.4, I.5, R.6, G.64, A.65, D.67, K.196 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:K.4 Hydrogen bonds: D:K.4, D:R.6, D:K.196, D:K.196 MPD.58: 5 residues within 4Å: Chain D: S.95, S.162, S.163, G.165, V.175 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:V.175 MPD.70: 6 residues within 4Å: Chain E: E.121, F.122, E.141, L.142, T.143 Ligands: MPD.85 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:E.121, E:F.122 Hydrogen bonds: E:E.141, E:E.141 MPD.72: 6 residues within 4Å: Chain E: K.4, R.6, E.48, A.65, D.67, K.196 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:K.4, E:R.6 Hydrogen bonds: E:R.6, E:R.6 MPD.85: 5 residues within 4Å: Chain F: E.121, E.141, L.142, T.143 Ligands: MPD.70 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:E.121, F:L.142 MPD.86: 7 residues within 4Å: Chain F: K.4, I.5, R.6, G.64, A.65, D.67, K.196 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:K.4 Hydrogen bonds: F:K.4, F:R.6, F:K.196, F:K.196 MPD.87: 5 residues within 4Å: Chain F: S.95, S.162, S.163, G.165, V.175 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:V.175

3 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.13: 5 residues within 4Å: Chain A: V.117, G.153, V.154, A.155, D.156 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.156 MRD.42: 5 residues within 4Å: Chain C: V.117, G.153, V.154, A.155, D.156 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.156 MRD.71: 5 residues within 4Å: Chain E: V.117, G.153, V.154, A.155, D.156 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lohkamp, B. et al., The Structure of Histidine Inhibited Hisg from Methanobacterium Thermoautotrophicum. To be Published

Release Date

2008-11-04

Peptides

ATP PHOSPHORIBOSYLTRANSFERASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

ATP PHOSPHORIBOSYLTRANSFERASE