SMTL ID : 8g8v.1

GTP Cyclohydrolase-IB with sodium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

homo-tetramer

Ligands

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

NA.1: 3 residues within 4Å: Chain A: C.188, H.200 Chain D: E.242 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.242 NA.9: 3 residues within 4Å: Chain B: C.188, H.200 Chain C: E.242 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.242 NA.18: 3 residues within 4Å: Chain B: E.242 Chain C: C.188, H.200 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.242 NA.26: 3 residues within 4Å: Chain A: E.242 Chain D: C.188, H.200 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.242

10 x SO3: SULFITE ION(Non-covalent)

SO3.2: 5 residues within 4Å: Chain A: F.255, V.256, E.257 Chain B: T.99, M.101 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.257, B:T.99 Water bridges: A:V.256, B:T.99 Salt bridges: A:E.257 SO3.6: 5 residues within 4Å: Chain A: E.139, T.166, F.177, D.209 Ligands: PG4.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.166, A:T.166 Salt bridges: A:E.139, A:D.209 SO3.10: 5 residues within 4Å: Chain A: T.99, M.101 Chain B: F.255, E.257 Ligands: EDO.4 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Water bridges: B:V.256 Salt bridges: B:E.257 Hydrogen bonds: A:T.99, A:T.99 SO3.14: 4 residues within 4Å: Chain B: R.67, P.143, E.162 Chain D: R.67 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D Water bridges: B:T.85 Salt bridges: B:E.162 Hydrogen bonds: D:R.67, D:R.67 SO3.15: 7 residues within 4Å: Chain B: E.139, T.164, T.166, F.177, K.179, D.209 Ligands: PG4.17 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.139, B:T.166, B:T.166, B:D.209 Salt bridges: B:E.139, B:D.209 SO3.19: 5 residues within 4Å: Chain C: F.255, V.256, E.257 Chain D: T.99, M.101 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:T.99, C:E.257 Water bridges: D:T.99, C:V.256 Salt bridges: C:E.257 SO3.23: 5 residues within 4Å: Chain C: E.139, T.166, F.177, D.209 Ligands: PG4.20 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:E.139, C:T.166 Water bridges: C:T.166, C:T.166 Salt bridges: C:E.139, C:D.209 SO3.27: 5 residues within 4Å: Chain C: T.99, M.101 Chain D: F.255, E.257 Ligands: EDO.21 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Water bridges: D:V.256 Salt bridges: D:E.257 Hydrogen bonds: C:T.99, C:T.99 SO3.31: 4 residues within 4Å: Chain B: R.67 Chain D: R.67, P.143, E.162 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:R.67, B:R.67 Water bridges: D:R.67 Salt bridges: D:E.162 SO3.32: 7 residues within 4Å: Chain D: E.139, T.164, T.166, F.177, K.179, D.209 Ligands: PG4.34 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:T.166, D:D.209 Water bridges: D:T.166, D:T.166 Salt bridges: D:E.139, D:D.209

4 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 9 residues within 4Å: Chain A: R.137, D.168, F.177, D.209, A.275, Y.276, V.277, R.297 Ligands: SO3.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.168, A:D.168 PG4.17: 9 residues within 4Å: Chain B: R.137, R.175, F.177, D.209, A.275, Y.276, V.277, R.297 Ligands: SO3.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.175 PG4.20: 9 residues within 4Å: Chain C: R.137, D.168, F.177, D.209, A.275, Y.276, V.277, R.297 Ligands: SO3.23 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.168 PG4.34: 9 residues within 4Å: Chain D: R.137, R.175, F.177, D.209, A.275, Y.276, V.277, R.297 Ligands: SO3.32 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.175

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

EDO.4: 6 residues within 4Å: Chain A: T.99, H.100, M.101, S.102 Ligands: EDO.7, SO3.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.99, A:M.101, A:S.102, A:S.102 EDO.5: 5 residues within 4Å: Chain A: R.67, P.143, E.162 Chain C: R.67 Ligands: EDO.22 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:R.67, A:E.162, C:R.67, C:R.67 Water bridges: A:E.162 EDO.7: 5 residues within 4Å: Chain A: H.100, S.102, R.103 Chain C: K.238 Ligands: EDO.4 No protein-ligand interaction detected (PLIP) EDO.8: 3 residues within 4Å: Chain A: V.72, L.165, V.218 No protein-ligand interaction detected (PLIP) EDO.12: 3 residues within 4Å: Chain B: R.239, P.240, K.243 No protein-ligand interaction detected (PLIP) EDO.13: 4 residues within 4Å: Chain B: P.57, H.91, P.93, A.94 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.94 EDO.16: 5 residues within 4Å: Chain B: D.160, Y.161, E.162, L.181 Chain C: N.288 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:D.160, B:E.162, C:N.288, C:N.288 EDO.21: 6 residues within 4Å: Chain C: T.99, H.100, M.101, S.102 Ligands: EDO.24, SO3.27 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.99, C:M.101, C:S.102, C:S.102 EDO.22: 5 residues within 4Å: Chain A: R.67 Chain C: R.67, P.143, E.162 Ligands: EDO.5 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:R.67, C:E.162, A:R.67, A:R.67 EDO.24: 5 residues within 4Å: Chain A: K.238 Chain C: H.100, S.102, R.103 Ligands: EDO.21 No protein-ligand interaction detected (PLIP) EDO.25: 3 residues within 4Å: Chain C: V.72, L.165, V.218 No protein-ligand interaction detected (PLIP) EDO.29: 3 residues within 4Å: Chain D: R.239, P.240, K.243 No protein-ligand interaction detected (PLIP) EDO.30: 4 residues within 4Å: Chain D: P.57, H.91, P.93, A.94 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:A.94 EDO.33: 5 residues within 4Å: Chain A: N.288 Chain D: D.160, Y.161, E.162, L.181 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:N.288, A:N.288, D:D.160, D:E.162

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.11: 4 residues within 4Å: Chain B: R.203, H.205, F.283 Chain C: F.283 No protein-ligand interaction detected (PLIP) PGE.28: 4 residues within 4Å: Chain A: F.283 Chain D: R.203, H.205, F.283 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Y. et al., Combatting melioidosis with chemical synthetic lethality. To Be Published

Release Date

2024-02-21

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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