SMTL ID : 3dkq.1

Crystal structure of Putative Oxygenase (YP_001051978.1) from SHEWANELLA BALTICA OS155 at 2.26 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

homo-hexamer

Ligands

6 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 5 residues within 4Å: Chain A: H.115, D.117, H.176 Ligands: IMD.2, IMD.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.115, A:D.117, A:H.176 NI.9: 4 residues within 4Å: Chain B: H.115, D.117, H.176 Ligands: IMD.10 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.115, B:D.117, B:H.176 NI.12: 5 residues within 4Å: Chain C: H.115, D.117, H.176 Ligands: IMD.13, IMD.14 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.115, C:D.117, C:H.176 NI.16: 5 residues within 4Å: Chain D: H.115, D.117, H.176 Ligands: IMD.17, IMD.18 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.115, D:D.117, D:H.176 NI.24: 4 residues within 4Å: Chain E: H.115, D.117, H.176 Ligands: IMD.25 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.115, E:D.117, E:H.176 NI.27: 5 residues within 4Å: Chain F: H.115, D.117, H.176 Ligands: IMD.28, IMD.29 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.115, F:D.117, F:H.176

12 x IMD: IMIDAZOLE(Non-covalent)

IMD.2: 10 residues within 4Å: Chain A: S.52, G.53, A.54, F.112, H.115, D.117, F.190, W.192 Ligands: NI.1, IMD.3 1 PLIP interactions: 1 interactions with chain A pi-Stacking: A:W.192 IMD.3: 8 residues within 4Å: Chain A: F.112, H.115, L.149, Y.170, H.176, V.178 Ligands: NI.1, IMD.2 1 PLIP interactions: 1 interactions with chain A pi-Stacking: A:F.112 IMD.10: 8 residues within 4Å: Chain B: N.104, Y.106, F.112, H.115, Y.170, H.176, V.178 Ligands: NI.9 1 PLIP interactions: 1 interactions with chain B pi-Stacking: B:F.112 IMD.11: 6 residues within 4Å: Chain B: E.142, N.143, Y.144, Q.145, S.183, G.184 No protein-ligand interaction detected (PLIP) IMD.13: 7 residues within 4Å: Chain C: F.112, H.115, D.117, R.121, W.192 Ligands: NI.12, IMD.14 No protein-ligand interaction detected (PLIP) IMD.14: 8 residues within 4Å: Chain C: F.112, H.115, L.149, Y.170, H.176, V.178 Ligands: NI.12, IMD.13 No protein-ligand interaction detected (PLIP) IMD.17: 10 residues within 4Å: Chain D: S.52, G.53, A.54, F.112, H.115, D.117, F.190, W.192 Ligands: NI.16, IMD.18 1 PLIP interactions: 1 interactions with chain D pi-Stacking: D:W.192 IMD.18: 8 residues within 4Å: Chain D: F.112, H.115, L.149, Y.170, H.176, V.178 Ligands: NI.16, IMD.17 1 PLIP interactions: 1 interactions with chain D pi-Stacking: D:F.112 IMD.25: 8 residues within 4Å: Chain E: N.104, Y.106, F.112, H.115, Y.170, H.176, V.178 Ligands: NI.24 2 PLIP interactions: 2 interactions with chain E Water bridges: E:T.135 pi-Stacking: E:F.112 IMD.26: 6 residues within 4Å: Chain E: E.142, N.143, Y.144, Q.145, S.183, G.184 No protein-ligand interaction detected (PLIP) IMD.28: 7 residues within 4Å: Chain F: F.112, H.115, D.117, R.121, W.192 Ligands: NI.27, IMD.29 No protein-ligand interaction detected (PLIP) IMD.29: 8 residues within 4Å: Chain F: F.112, H.115, L.149, Y.170, H.176, V.178 Ligands: NI.27, IMD.28 No protein-ligand interaction detected (PLIP)

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: R.198, E.242 Chain F: Q.202, R.239, W.240, S.241, E.242 Ligands: GOL.30 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:Q.202, F:Q.202, A:E.242 GOL.5: 5 residues within 4Å: Chain A: Q.202, R.239, W.240, S.241, E.242 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.202, A:Q.202, A:S.241 GOL.6: 9 residues within 4Å: Chain A: I.116, Q.152, S.173, L.175 Chain C: Q.208 Chain F: Q.224, F.227, N.228, G.231 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain F Hydrogen bonds: A:Q.152, F:Q.224, F:N.228 GOL.7: 10 residues within 4Å: Chain A: Q.18, G.19, M.20, L.21, I.151, D.153, Y.155, G.156, Q.157, Q.158 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.153, A:Q.158 GOL.8: 6 residues within 4Å: Chain A: D.210, I.213, Q.214, S.230, Y.233, H.234 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.214, A:S.230 Water bridges: A:Y.233 GOL.15: 7 residues within 4Å: Chain A: D.199, Q.202 Chain B: R.239 Chain C: D.199, Q.202 Chain F: R.239 Ligands: GOL.19 8 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C, 2 interactions with chain B, 1 interactions with chain F Hydrogen bonds: A:D.199, A:Q.202, C:Q.202, B:R.239, F:R.239 Water bridges: A:D.199, C:Q.202, B:R.239 GOL.19: 8 residues within 4Å: Chain C: Q.202, R.239, W.240, S.241, E.242 Chain D: R.198, E.242 Ligands: GOL.15 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:E.242, C:Q.202, C:Q.202 GOL.20: 5 residues within 4Å: Chain D: Q.202, R.239, W.240, S.241, E.242 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.202, D:Q.202, D:S.241 GOL.21: 9 residues within 4Å: Chain C: Q.224, F.227, N.228, G.231 Chain D: I.116, Q.152, S.173, L.175 Chain F: Q.208 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Q.224, C:N.228, D:Q.152 GOL.22: 10 residues within 4Å: Chain D: Q.18, G.19, M.20, L.21, I.151, D.153, Y.155, G.156, Q.157, Q.158 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.153, D:Q.158 GOL.23: 6 residues within 4Å: Chain D: D.210, I.213, Q.214, S.230, Y.233, H.234 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.214, D:S.230 Water bridges: D:Y.233, D:Y.233, D:Y.233 GOL.30: 7 residues within 4Å: Chain C: R.239 Chain D: D.199, Q.202 Chain E: R.239 Chain F: D.199, Q.202 Ligands: GOL.4 7 PLIP interactions: 2 interactions with chain F, 2 interactions with chain D, 1 interactions with chain C, 2 interactions with chain E Hydrogen bonds: F:Q.202, D:Q.202, C:R.239, E:R.239 Water bridges: F:Q.202, D:D.199, E:R.239

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of Putative Oxygenase (YP_001051978.1) from SHEWANELLA BALTICA OS155 at 2.26 A resolution. To be published

Release Date

2008-08-12

Peptides

PKHD-type hydroxylase Sbal_3634: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

PKHD-type hydroxylase Sbal_3634