SMTL ID : 2o1q.1

CRYSTAL STRUCTURE OF A PUTATIVE ACETYLACETONE DIOXYGENASE (MPE_A3659) FROM METHYLIBIUM PETROLEIPHILUM PM1 AT 1.50 A RESOLUTION

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.60, H.62, H.102 Ligands: ACT.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.60, A:H.62, A:H.102, ACT.5 ZN.9: 4 residues within 4Å: Chain B: H.60, H.62, H.102 Ligands: ACT.11 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.60, B:H.62, B:H.102, ACT.11 ZN.10: 3 residues within 4Å: Chain B: V.133, E.137, D.138 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.137, B:D.138, H2O.5, H2O.6, H2O.7, H2O.8 ZN.14: 4 residues within 4Å: Chain C: H.60, H.62, H.102 Ligands: ACT.18 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.60, C:H.62, C:H.102 ZN.22: 4 residues within 4Å: Chain D: H.60, H.62, H.102 Ligands: ACT.24 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:H.60, D:H.62, D:H.102, ACT.24 ZN.23: 3 residues within 4Å: Chain D: V.133, E.137, D.138 6 PLIP interactions: 2 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:E.137, D:D.138, H2O.13, H2O.14, H2O.15, H2O.16

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 5 residues within 4Å: Chain A: G.135, W.136, E.137, D.138 Chain B: N.99 Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain C: G.135, W.136, E.137, D.138 Chain D: N.99 Ligand excluded by PLIP

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

ACT.3: 1 residues within 4Å: Chain A: D.103 No protein-ligand interaction detected (PLIP) ACT.4: 8 residues within 4Å: Chain A: F.22, P.23, F.26, W.33, I.134, D.138, A.139, A.142 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.22, A:W.33, A:I.134 Hydrogen bonds: A:D.138 Water bridges: A:A.142 ACT.5: 7 residues within 4Å: Chain A: H.60, H.62, H.102, T.105, F.113, M.115 Ligands: ZN.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.105, A:F.113 Hydrogen bonds: A:T.105 Salt bridges: A:H.60, A:H.62, A:H.102 ACT.11: 7 residues within 4Å: Chain B: H.60, H.62, H.102, T.105, F.113, M.115 Ligands: ZN.9 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.113 Hydrogen bonds: B:T.105 Salt bridges: B:H.60, B:H.62, B:H.102 ACT.12: 3 residues within 4Å: Chain B: E.112 Chain D: F.69, P.91 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.69, D:P.91 ACT.16: 1 residues within 4Å: Chain C: D.103 No protein-ligand interaction detected (PLIP) ACT.17: 8 residues within 4Å: Chain C: F.22, P.23, F.26, W.33, I.134, D.138, A.139, A.142 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.22, C:W.33, C:I.134 Hydrogen bonds: C:D.138 Water bridges: C:A.142 ACT.18: 7 residues within 4Å: Chain C: H.60, H.62, H.102, T.105, F.113, M.115 Ligands: ZN.14 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:T.105, C:F.113 Salt bridges: C:H.60, C:H.62, C:H.102 ACT.24: 7 residues within 4Å: Chain D: H.60, H.62, H.102, T.105, F.113, M.115 Ligands: ZN.22 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:F.113 Salt bridges: D:H.60, D:H.62, D:H.102 ACT.25: 3 residues within 4Å: Chain B: F.69, P.91 Chain D: E.112 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.69, B:P.91

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

PG4.6: 8 residues within 4Å: Chain A: E.10, K.20, L.35, L.36, H.37, V.38, W.143 Chain D: K.4 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:K.20, A:K.20, A:V.38, D:K.4 Water bridges: A:E.10 PG4.7: 3 residues within 4Å: Chain A: D.76, K.104, E.106 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.104 Hydrogen bonds: A:D.76, A:D.76 PG4.8: 6 residues within 4Å: Chain A: S.5, K.6, I.7, K.8, E.9 Chain C: R.78 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.78, C:G.84, A:K.6 PG4.13: 7 residues within 4Å: Chain B: K.6, I.7, E.9 Chain D: R.78, N.99, A.100, R.101 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:K.6 Hydrogen bonds: D:R.101, D:R.101 PG4.19: 8 residues within 4Å: Chain B: K.4 Chain C: E.10, K.20, L.35, L.36, H.37, V.38, W.143 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:K.20, C:K.20, C:H.37, C:V.38, B:K.4 PG4.20: 3 residues within 4Å: Chain C: D.76, K.104, E.106 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:K.104 Hydrogen bonds: C:D.76, C:E.106 PG4.21: 6 residues within 4Å: Chain A: R.78 Chain C: S.5, K.6, I.7, K.8, E.9 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.78, A:G.84, C:K.6 PG4.26: 7 residues within 4Å: Chain B: R.78, N.99, A.100, R.101 Chain D: K.6, I.7, E.9 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:R.101, B:R.101 Hydrophobic interactions: D:K.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of putative acetyl/propionyl-CoA carboxylase, alpha subunit (ZP_00243239.1) from Rubrivivax gelatinosus PM1 (Methylobium petroleophilum PM1) at 1.50 A resolution. To be published

Release Date

2007-01-23

Peptides

putative acetyl/propionyl-CoA carboxylase, alpha subunit: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

putative acetyl/propionyl-CoA carboxylase, alpha subunit