SMTL ID : 6otv.1 (1 other biounit)

Crystal structure of putative isomerase EC2056

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

5 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 8 residues within 4Å: Chain A: P.91, N.92, M.196, K.250, Y.267, A.278, T.280 Ligands: PO4.7 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.91 Hydrogen bonds: A:Y.267, A:T.280 Water bridges: A:K.250, A:K.250 Salt bridges: A:K.250 ACT.5: 2 residues within 4Å: Chain A: N.43, L.45 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.43 ACT.6: 6 residues within 4Å: Chain A: Y.143, E.144, T.155, A.156, R.340 Ligands: EDO.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.144 Hydrogen bonds: A:Y.143 Water bridges: A:T.155 ACT.15: 8 residues within 4Å: Chain B: P.91, N.92, M.196, K.250, Y.267, A.278, T.280 Ligands: PO4.18 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.91 Water bridges: B:K.250 ACT.16: 5 residues within 4Å: Chain B: Y.143, E.144, T.155, R.340 Ligands: EDO.21 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.143, B:R.340

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

EDO.2: 8 residues within 4Å: Chain A: F.163, L.164, N.165, A.166, A.167, T.329, L.331 Chain B: P.69 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.163, A:A.166, A:A.167, A:T.329 EDO.3: 10 residues within 4Å: Chain A: R.10, A.147, I.149, V.152, P.153, G.154, T.155, A.156, T.338 Ligands: ACT.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.10, A:R.10, A:I.149 EDO.4: 3 residues within 4Å: Chain A: R.148, G.154 Ligands: EDO.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.154 EDO.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.10: 7 residues within 4Å: Chain A: L.20, A.21, E.22, I.63, S.64, R.65, L.109 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.21, A:E.22, A:I.63, A:R.65 EDO.11: 5 residues within 4Å: Chain A: K.173, V.174, F.175, D.327, T.329 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.174, A:F.175, A:F.175 EDO.12: 3 residues within 4Å: Chain A: Y.143, R.340, K.341 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.340, A:K.341, A:K.341 EDO.13: 10 residues within 4Å: Chain A: S.322, N.323, E.324, G.325, T.330, R.332 Chain B: S.66, S.67, D.68, P.69 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.322, A:E.324, A:G.325, A:T.330, B:S.67 EDO.14: 8 residues within 4Å: Chain A: R.148, I.149, D.150, G.151, V.152, P.153, G.154 Ligands: EDO.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.148, A:I.149, A:G.151, A:V.152, A:G.154 Water bridges: A:I.149 EDO.17: 8 residues within 4Å: Chain A: P.69 Chain B: F.163, L.164, N.165, A.166, A.167, T.329, L.331 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.163, B:A.166, B:A.167, B:T.329 EDO.20: 7 residues within 4Å: Chain A: S.67, P.69 Chain B: S.322, N.323, E.324, T.330, R.332 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.323, B:E.324, B:G.325 EDO.21: 4 residues within 4Å: Chain B: Y.143, R.340, K.341 Ligands: ACT.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.340, B:K.341 EDO.22: 4 residues within 4Å: Chain B: K.173, V.174, F.175, T.329 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.174, B:F.175, B:F.175 EDO.23: 6 residues within 4Å: Chain B: L.20, A.21, E.22, S.64, R.65, L.109 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.21, B:E.22, B:I.63, B:R.65 EDO.24: 4 residues within 4Å: Chain B: D.44, L.45, G.52, G.53 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.44

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.7: 8 residues within 4Å: Chain A: N.92, C.93, G.94, N.95, L.277, A.278, I.279 Ligands: ACT.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.92, A:G.94, A:N.95, A:N.95, A:I.279 PO4.8: 4 residues within 4Å: Chain A: P.55, I.81, V.82, H.83 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.82, A:H.83 Water bridges: A:V.80 Salt bridges: A:H.83 PO4.18: 8 residues within 4Å: Chain B: N.92, C.93, G.94, N.95, L.277, A.278, I.279 Ligands: ACT.15 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.94, B:N.95, B:N.95, B:I.279 PO4.19: 4 residues within 4Å: Chain B: P.55, I.81, V.82, H.83 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.82, B:H.83 Salt bridges: B:H.83

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chang, C. et al., Crystal structure of putative isomerase EC2056. To Be Published

Release Date

2019-05-15

Peptides

Putative isomerase YbhH: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Putative isomerase YbhH

Related Entries With Identical Sequence