SMTL ID : 2br4.1

cmcI-D160 Mg-SAM

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

homo-hexamer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.160, H.162, D.187 Ligands: P4C.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.160, A:D.187 MG.5: 4 residues within 4Å: Chain B: D.160, H.162, D.187 Ligands: P4C.8 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.187, H2O.4 MG.9: 4 residues within 4Å: Chain C: D.160, E.186, D.187, Q.223 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.186, C:D.187 MG.11: 4 residues within 4Å: Chain D: D.160, E.186, D.187, Q.223 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.160, D:D.187 MG.15: 5 residues within 4Å: Chain E: D.160, H.162, D.187 Ligands: P4C.4, SAM.16 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.160, E:D.187 MG.17: 5 residues within 4Å: Chain F: D.160, H.162, D.187 Ligands: P4C.14, SAM.18 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.187

6 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.2: 19 residues within 4Å: Chain A: L.18, L.64, K.65, E.87, G.89, V.90, Y.91, S.95, D.116, R.117, R.121, G.137, D.138, C.139, S.140, D.160, A.161, A.163 Ligands: P4C.4 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:D.160 Hydrogen bonds: A:L.64, A:G.89, A:Y.91, A:S.95, A:S.95, A:R.117, A:R.121, A:R.121, A:D.138, A:C.139, A:S.140, A:D.160 Water bridges: A:G.93, A:E.186 Salt bridges: A:K.65, A:D.160 pi-Cation interactions: A:R.117 SAM.6: 19 residues within 4Å: Chain B: L.18, L.64, K.65, E.87, G.89, V.90, Y.91, N.92, S.95, D.116, R.117, R.121, G.137, D.138, C.139, D.160, A.161, A.163 Ligands: P4C.8 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:L.64, B:G.89, B:Y.91, B:N.92, B:S.95, B:S.95, B:R.117, B:R.121, B:D.138, B:C.139 Water bridges: B:G.93, B:D.116, B:R.117, B:D.118 Salt bridges: B:K.65, B:D.160 SAM.10: 19 residues within 4Å: Chain C: L.18, L.64, K.65, E.87, G.89, V.90, Y.91, S.95, D.116, R.117, R.121, G.137, D.138, C.139, S.140, D.160, A.161, A.163 Ligands: P4C.8 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:L.64, C:K.65, C:G.89, C:Y.91, C:S.95, C:S.95, C:R.117, C:R.121, C:R.121, C:D.138, C:C.139, C:S.140, C:D.160, C:D.160 Salt bridges: C:K.65 pi-Cation interactions: C:R.117 SAM.12: 18 residues within 4Å: Chain D: L.18, L.64, K.65, E.87, G.89, V.90, Y.91, S.95, D.116, R.117, R.121, G.137, D.138, C.139, D.160, A.161, A.163 Ligands: P4C.14 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:Y.91 Hydrogen bonds: D:L.64, D:K.65, D:K.65, D:K.65, D:Y.91, D:S.95, D:R.117, D:R.121, D:R.121, D:D.138, D:C.139 pi-Cation interactions: D:R.117 SAM.16: 18 residues within 4Å: Chain E: L.18, L.64, K.65, E.87, G.89, V.90, Y.91, S.95, D.116, R.117, R.121, D.138, C.139, D.160, A.161, A.163 Ligands: P4C.4, MG.15 15 PLIP interactions: 15 interactions with chain E Hydrophobic interactions: E:L.64, E:D.160 Hydrogen bonds: E:L.64, E:G.89, E:Y.91, E:S.95, E:S.95, E:R.117, E:R.121, E:R.121, E:D.138, E:D.138, E:C.139 Salt bridges: E:K.65 pi-Cation interactions: E:R.117 SAM.18: 17 residues within 4Å: Chain F: L.18, L.64, K.65, E.87, G.89, V.90, Y.91, S.95, D.116, R.117, R.121, D.138, C.139, D.160, A.161, A.163 Ligands: MG.17 14 PLIP interactions: 14 interactions with chain F Hydrophobic interactions: F:L.64 Hydrogen bonds: F:L.64, F:K.65, F:Y.91, F:S.95, F:S.95, F:R.117, F:R.121, F:D.138, F:C.139, F:D.160 Water bridges: F:S.95 Salt bridges: F:K.65 pi-Cation interactions: F:R.117

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

PEG.3: 4 residues within 4Å: Chain A: N.13, R.16 Chain E: N.13, R.16 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:N.13, A:N.13 PEG.7: 5 residues within 4Å: Chain B: N.13, R.16 Chain C: N.13, R.16 Ligands: P4C.8 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:R.16, C:N.13 PEG.13: 4 residues within 4Å: Chain D: N.13, R.16 Chain F: N.13, R.16 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:N.13, F:N.13

3 x P4C: O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL(Non-covalent)

P4C.4: 16 residues within 4Å: Chain A: R.16, G.17, L.18, H.162, Y.191, Y.195 Chain E: R.16, G.17, L.18, M.188, Y.191, Y.195 Ligands: MG.1, SAM.2, MG.15, SAM.16 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain A Hydrogen bonds: E:R.16, E:R.16, A:R.16, A:H.162, A:Y.195 P4C.8: 17 residues within 4Å: Chain B: R.16, G.17, L.18, H.162, M.188, Y.191, Y.195 Chain C: R.16, G.17, L.18, M.188, Y.191, Y.195 Ligands: MG.5, SAM.6, PEG.7, SAM.10 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:R.16, B:R.16, B:Y.195, C:R.16, C:Y.195 P4C.14: 13 residues within 4Å: Chain D: R.16, H.162, M.188, Y.191, Y.195 Chain F: R.16, G.17, H.162, M.188, Y.191, Y.195 Ligands: SAM.12, MG.17 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:R.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oster, L.M. et al., Insights Into Cephamycin Biosynthesis: The Crystal Structure of Cmci from Streptomyces Clavuligerus. J.Mol.Biol. (2006)

Release Date

2006-03-15

Peptides

CEPHALOSPORIN HYDROXYLASE CMCI: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

CEPHALOSPORIN HYDROXYLASE CMCI

Related Entries With Identical Sequence