SMTL ID : 6nfp.1

1.7 Angstrom Resolution Crystal Structure of Arginase from Bacillus subtilis subsp. subtilis str. 168

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-hexamer

Ligands

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

CL.1: 5 residues within 4Å: Chain A: T.130, L.131, E.132, G.151, H.152 Ligand excluded by PLIP CL.2: 5 residues within 4Å: Chain A: P.14, M.15, D.16, L.17, I.55 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: K.192, V.193, Y.194 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: A.34, R.39 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain B: T.130, L.131, G.151, H.152 Ligand excluded by PLIP CL.38: 6 residues within 4Å: Chain C: T.130, L.131, E.132, G.151, H.152 Ligands: URE.47 Ligand excluded by PLIP CL.39: 3 residues within 4Å: Chain C: R.57, E.58 Ligands: GOA.53 Ligand excluded by PLIP CL.40: 1 residues within 4Å: Chain C: A.34 Ligand excluded by PLIP CL.57: 4 residues within 4Å: Chain D: T.130, L.131, G.151, H.152 Ligand excluded by PLIP CL.70: 2 residues within 4Å: Chain A: V.243 Chain E: Y.248 Ligand excluded by PLIP

3 x NA: SODIUM ION(Non-functional Binders)

NA.5: 2 residues within 4Å: Chain A: D.277 Chain D: D.277 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.277 NA.21: 2 residues within 4Å: Chain B: D.277 Chain C: D.277 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.277 NA.71: 2 residues within 4Å: Chain E: D.277 Chain F: D.277 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.277

12 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 6 residues within 4Å: Chain A: D.123, H.125, D.226, D.228 Ligands: MG.7, SO4.18 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.123, A:H.125, A:D.226, A:D.228, A:D.228 MG.7: 6 residues within 4Å: Chain A: H.100, D.123, D.127, D.226 Ligands: MG.6, SO4.18 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.100, A:D.123, A:D.127, A:D.226 MG.22: 6 residues within 4Å: Chain B: D.123, H.125, D.226, D.228 Ligands: MG.23, SO4.32 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.123, B:H.125, B:D.226, B:D.228, B:D.228 MG.23: 6 residues within 4Å: Chain B: H.100, D.123, D.127, D.226 Ligands: MG.22, SO4.32 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.100, B:D.123, B:D.127, B:D.226 MG.41: 6 residues within 4Å: Chain C: D.123, H.125, D.226, D.228 Ligands: MG.42, SO4.55 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.123, C:H.125, C:D.226, C:D.228, C:D.228 MG.42: 6 residues within 4Å: Chain C: H.100, D.123, D.127, D.226 Ligands: MG.41, SO4.55 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.100, C:D.123, C:D.127, C:D.226 MG.58: 6 residues within 4Å: Chain D: D.123, H.125, D.226, D.228 Ligands: MG.59, SO4.66 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.123, D:H.125, D:D.226, D:D.228, D:D.228 MG.59: 6 residues within 4Å: Chain D: H.100, D.123, D.127, D.226 Ligands: MG.58, SO4.66 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.100, D:D.123, D:D.127, D:D.226 MG.72: 6 residues within 4Å: Chain E: D.123, H.125, D.226, D.228 Ligands: MG.73, SO4.81 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.123, E:H.125, E:D.226, E:D.228, E:D.228 MG.73: 6 residues within 4Å: Chain E: H.100, D.123, D.127, D.226 Ligands: MG.72, SO4.81 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.100, E:D.123, E:D.127, E:D.226 MG.84: 6 residues within 4Å: Chain F: D.123, H.125, D.226, D.228 Ligands: MG.85, SO4.93 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.123, F:H.125, F:D.226, F:D.228, F:D.228 MG.85: 6 residues within 4Å: Chain F: H.100, D.123, D.127, D.226 Ligands: MG.84, SO4.93 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.100, F:D.123, F:D.127, F:D.226

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

FMT.8: 4 residues within 4Å: Chain A: Y.259, I.264, L.293, L.294 No protein-ligand interaction detected (PLIP) FMT.9: 7 residues within 4Å: Chain A: A.111, Y.114, D.115, N.116, L.117, K.164, K.166 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.111, A:L.117 Water bridges: A:N.169 FMT.24: 5 residues within 4Å: Chain B: M.4, Y.259, I.264, L.293, L.294 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.262 FMT.25: 5 residues within 4Å: Chain A: L.299 Chain B: M.191, K.192, V.193 Ligands: FMT.26 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.193 FMT.26: 5 residues within 4Å: Chain B: K.192, V.193, Y.194, E.198 Ligands: FMT.25 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.198 FMT.60: 3 residues within 4Å: Chain D: M.4, I.264, L.293 No protein-ligand interaction detected (PLIP) FMT.61: 5 residues within 4Å: Chain D: H.125, N.129, S.177, D.179, E.182 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.129, D:D.179 Water bridges: D:D.127 FMT.62: 5 residues within 4Å: Chain C: L.299 Chain D: M.191, K.192, V.193 Ligands: FMT.63 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:V.193 FMT.63: 4 residues within 4Å: Chain D: V.193, Y.194, E.210 Ligands: FMT.62 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.192, D:V.193 FMT.74: 3 residues within 4Å: Chain E: I.264, L.293, L.294 1 PLIP interactions: 1 interactions with chain E Water bridges: E:G.262 FMT.75: 5 residues within 4Å: Chain B: L.299 Chain E: M.191, K.192, V.193 Ligands: URE.79 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:V.193, E:V.193 FMT.76: 7 residues within 4Å: Chain E: A.111, Y.114, D.115, N.116, L.117, K.164, K.166 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:L.117, E:K.166 Water bridges: E:N.169 FMT.77: 4 residues within 4Å: Chain E: G.149, I.150, G.151, E.153 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:G.151 FMT.86: 4 residues within 4Å: Chain F: A.34, R.39, K.284, E.288 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.39, F:K.284 FMT.87: 3 residues within 4Å: Chain F: K.166, P.167, E.168 No protein-ligand interaction detected (PLIP)

16 x URE: UREA(Non-functional Binders)

URE.10: 6 residues within 4Å: Chain A: L.128, T.130, T.133, A.145, I.150, Y.185 Ligand excluded by PLIP URE.11: 3 residues within 4Å: Chain A: L.212, D.213, S.216 Ligand excluded by PLIP URE.12: 5 residues within 4Å: Chain A: Y.248, H.252, E.288 Chain B: R.176, V.243 Ligand excluded by PLIP URE.27: 5 residues within 4Å: Chain B: A.34, R.39, K.284, V.287, E.288 Ligand excluded by PLIP URE.28: 1 residues within 4Å: Chain B: E.159 Ligand excluded by PLIP URE.29: 3 residues within 4Å: Chain B: E.132, T.133, S.134 Ligand excluded by PLIP URE.43: 7 residues within 4Å: Chain C: Y.248, H.252, E.288 Chain D: R.176, V.243 Ligands: URE.44, EDO.51 Ligand excluded by PLIP URE.44: 4 residues within 4Å: Chain C: R.39, E.288, E.291 Ligands: URE.43 Ligand excluded by PLIP URE.45: 2 residues within 4Å: Chain C: K.192, Y.214 Ligand excluded by PLIP URE.46: 4 residues within 4Å: Chain C: K.192, V.193, Y.194, E.198 Ligand excluded by PLIP URE.47: 4 residues within 4Å: Chain C: T.130, E.132, G.151 Ligands: CL.38 Ligand excluded by PLIP URE.48: 6 residues within 4Å: Chain C: E.48, L.50, K.85, V.86, E.89, K.91 Ligand excluded by PLIP URE.78: 5 residues within 4Å: Chain E: A.34, R.39, K.284, V.287, E.288 Ligand excluded by PLIP URE.79: 5 residues within 4Å: Chain E: K.192, V.193, Y.194, E.198 Ligands: FMT.75 Ligand excluded by PLIP URE.88: 4 residues within 4Å: Chain F: K.112, H.113, Y.114, D.115 Ligand excluded by PLIP URE.89: 3 residues within 4Å: Chain E: I.275, L.276 Chain F: Y.33 Ligand excluded by PLIP

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

EDO.13: 4 residues within 4Å: Chain A: K.281, K.284, T.285 Chain B: V.243 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.285 EDO.14: 2 residues within 4Å: Chain A: P.232, P.241 1 PLIP interactions: 1 interactions with chain A Water bridges: A:V.243 EDO.15: 3 residues within 4Å: Chain A: S.41, G.44, Y.45 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.41 EDO.16: 5 residues within 4Å: Chain A: S.29, R.32, D.52 Chain D: R.21, D.25 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Water bridges: D:P.14, D:D.16, D:R.21, A:D.52 Hydrogen bonds: A:R.32 EDO.17: 3 residues within 4Å: Chain A: M.43, L.294, G.295 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.294 Water bridges: A:K.297 EDO.30: 5 residues within 4Å: Chain B: G.149, I.150, G.151, E.153 Ligands: PEG.37 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.151, B:E.153 EDO.31: 7 residues within 4Å: Chain B: Y.248, H.252, E.288 Chain E: R.176, V.242, V.243 Ligands: EDO.80 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain B Hydrogen bonds: E:R.176, B:Y.248, B:H.252 EDO.49: 3 residues within 4Å: Chain C: Y.259, I.264, L.293 2 PLIP interactions: 2 interactions with chain C Water bridges: C:Y.45, C:G.262 EDO.50: 9 residues within 4Å: Chain C: R.176, M.196, D.200, G.244 Chain F: Y.248, R.249, H.252, L.298 Ligands: SO4.54 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.249, F:H.252 EDO.51: 8 residues within 4Å: Chain C: Y.248, R.249, H.252 Chain D: R.176, M.196, D.200, G.244 Ligands: URE.43 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:H.252, D:D.200, D:V.243 Water bridges: D:D.200 EDO.64: 4 residues within 4Å: Chain D: G.149, I.150, G.151, E.153 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.151 EDO.80: 9 residues within 4Å: Chain B: Y.248, R.249, H.252 Chain E: R.176, M.196, D.200, V.243, G.244 Ligands: EDO.31 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain B Water bridges: E:D.200 Hydrogen bonds: B:R.249 EDO.90: 9 residues within 4Å: Chain D: Y.248, R.249, H.252 Chain F: R.176, M.196, D.200, V.243, G.244 Ligands: GOA.65 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain F Hydrogen bonds: D:H.252, F:D.200, F:V.243 EDO.91: 3 residues within 4Å: Chain F: G.149, I.150, G.151 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:G.151

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

SO4.18: 11 residues within 4Å: Chain A: R.22, D.123, H.125, D.127, H.140, D.226, D.228, T.240, E.271 Ligands: MG.6, MG.7 Ligand excluded by PLIP SO4.19: 4 residues within 4Å: Chain A: D.213, Y.214, S.216, A.217 Ligand excluded by PLIP SO4.32: 12 residues within 4Å: Chain B: R.22, H.100, D.123, H.125, D.127, H.140, D.226, D.228, T.240, E.271 Ligands: MG.22, MG.23 Ligand excluded by PLIP SO4.33: 6 residues within 4Å: Chain B: D.16, L.17, G.18, A.20, R.21, N.68 Ligand excluded by PLIP SO4.34: 4 residues within 4Å: Chain B: I.87, K.90, H.113, Y.114 Ligand excluded by PLIP SO4.35: 5 residues within 4Å: Chain B: L.128, T.130, I.150, G.181, Y.185 Ligand excluded by PLIP SO4.54: 8 residues within 4Å: Chain C: R.176, V.242, V.243 Chain F: Y.248, H.252, E.288, L.298 Ligands: EDO.50 Ligand excluded by PLIP SO4.55: 12 residues within 4Å: Chain C: R.22, H.100, D.123, H.125, D.127, H.140, D.226, D.228, T.240, E.271 Ligands: MG.41, MG.42 Ligand excluded by PLIP SO4.56: 6 residues within 4Å: Chain C: L.128, T.130, A.145, I.150, G.181, Y.185 Ligand excluded by PLIP SO4.66: 13 residues within 4Å: Chain D: R.22, H.100, D.123, H.125, D.127, H.140, G.141, D.226, D.228, T.240, E.271 Ligands: MG.58, MG.59 Ligand excluded by PLIP SO4.67: 3 residues within 4Å: Chain D: K.90, H.113, Y.114 Ligand excluded by PLIP SO4.68: 7 residues within 4Å: Chain D: D.16, L.17, G.18, Q.19, A.20, R.21, N.68 Ligand excluded by PLIP SO4.69: 6 residues within 4Å: Chain D: L.128, T.130, A.145, I.150, G.181, Y.185 Ligand excluded by PLIP SO4.81: 13 residues within 4Å: Chain E: R.22, H.100, D.123, H.125, D.127, H.140, G.141, D.226, D.228, T.240, E.271 Ligands: MG.72, MG.73 Ligand excluded by PLIP SO4.82: 7 residues within 4Å: Chain E: L.128, T.130, T.133, A.145, I.150, G.181, Y.185 Ligand excluded by PLIP SO4.83: 4 residues within 4Å: Chain E: D.5, M.43, G.44, Y.45 Ligand excluded by PLIP SO4.93: 12 residues within 4Å: Chain F: R.22, H.100, D.123, H.125, D.127, H.140, D.226, D.228, T.240, E.271 Ligands: MG.84, MG.85 Ligand excluded by PLIP SO4.94: 6 residues within 4Å: Chain F: L.128, T.130, A.145, I.150, G.181, Y.185 Ligand excluded by PLIP

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

PEG.36: 3 residues within 4Å: Chain B: I.150, Y.185, S.189 No protein-ligand interaction detected (PLIP) PEG.37: 7 residues within 4Å: Chain B: L.148, G.149, I.150, V.156, A.162, P.163 Ligands: EDO.30 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.153

4 x GOA: GLYCOLIC ACID(Non-covalent)

GOA.52: 3 residues within 4Å: Chain B: R.32, I.37 Chain C: R.21 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Salt bridges: C:R.21 Water bridges: B:D.49 GOA.53: 6 residues within 4Å: Chain C: D.16, L.17, G.18, R.21, N.68 Ligands: CL.39 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.16, C:G.18 Water bridges: C:N.68 GOA.65: 8 residues within 4Å: Chain D: Y.248, H.252, E.288, L.298 Chain F: R.176, V.242, V.243 Ligands: EDO.90 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain F Water bridges: D:E.288, D:K.296 Salt bridges: D:H.252 Hydrogen bonds: F:R.176, F:V.243 GOA.92: 5 residues within 4Å: Chain F: F.92, Y.259, I.264, L.293, L.294 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:L.293 Water bridges: F:G.262

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Minasov, G. et al., 1.7 Angstrom Resolution Crystal Structure of Arginase from Bacillus subtilis subsp. subtilis str. 168. To Be Published

Release Date

2019-01-02

Peptides

Arginase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Arginase