SMTL ID : 5k9g.1

Crystal Structure of GTP Cyclohydrolase-IB with Tris

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: C.147, H.159 Chain C: E.201 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: A:C.147, A:H.159, C:E.201, H2O.3, H2O.20 ZN.4: 4 residues within 4Å: Chain B: C.147, H.159 Chain D: E.201 Ligands: TRS.5 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Metal complexes: B:C.147, B:H.159, D:E.201 ZN.13: 3 residues within 4Å: Chain A: E.201 Chain C: C.147, H.159 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: C:C.147, C:H.159, A:E.201, H2O.5, H2O.18 ZN.16: 4 residues within 4Å: Chain B: E.201 Chain D: C.147, H.159 Ligands: TRS.17 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Metal complexes: D:C.147, D:H.159, B:E.201

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

EDO.2: 9 residues within 4Å: Chain A: F.76, H.135, S.136, M.137, L.169, T.170, S.171, E.174, V.175 Ligand excluded by PLIP EDO.3: 4 residues within 4Å: Chain A: F.76, A.77, H.80, E.174 Ligand excluded by PLIP EDO.6: 9 residues within 4Å: Chain B: F.76, H.135, S.136, M.137, L.169, T.170, S.171, E.174, V.175 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain B: S.168, L.169, T.170, S.234, F.235, V.236 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain B: K.107, T.108, Q.191, Y.193 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain B: T.125, E.127, G.134, H.135, S.136, T.170 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain B: K.151, Y.209, E.210 Chain D: Y.156 Ligand excluded by PLIP EDO.11: 7 residues within 4Å: Chain B: K.33, T.34, D.75, F.76, G.176, I.177, E.178 Ligand excluded by PLIP EDO.14: 9 residues within 4Å: Chain C: F.76, H.135, S.136, M.137, L.169, T.170, S.171, E.174, V.175 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain C: F.76, A.77, H.80, E.174 Ligand excluded by PLIP EDO.18: 9 residues within 4Å: Chain D: F.76, H.135, S.136, M.137, L.169, T.170, S.171, E.174, V.175 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain D: S.168, L.169, T.170, S.234, F.235, V.236 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain D: K.107, T.108, Q.191, Y.193 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain D: T.125, E.127, G.134, H.135, S.136, T.170 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain B: Y.156 Chain D: K.151, Y.209, E.210 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain D: K.33, T.34, D.75, F.76, G.176, I.177, E.178 Ligand excluded by PLIP

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.5: 9 residues within 4Å: Chain A: M.60 Chain B: C.147, C.149, H.159, E.243, I.245, H.246 Chain D: E.201 Ligands: ZN.4 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.243, B:H.246 Water bridges: B:E.216 TRS.17: 9 residues within 4Å: Chain B: E.201 Chain C: M.60 Chain D: C.147, C.149, H.159, E.243, I.245, H.246 Ligands: ZN.16 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.243, D:E.243, D:H.246 Water bridges: D:E.216

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

FMT.12: 6 residues within 4Å: Chain B: C.147, H.159, Q.161, K.213, N.241, E.243 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.145, B:Q.161, B:N.241 Water bridges: B:V.215 FMT.24: 6 residues within 4Å: Chain D: C.147, H.159, Q.161, K.213, N.241, E.243 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.145, D:Q.161, D:N.241 Water bridges: D:V.215

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Paranagama, N. et al., Mechanism and catalytic strategy of the prokaryotic-specific GTP cyclohydrolase-IB. Biochem.J. (2017)

Release Date

2016-09-07

Peptides

GTP cyclohydrolase FolE2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

GTP cyclohydrolase FolE2

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