SMTL ID : 2xvx.1

COBALT CHELATASE CBIK (PERIPLASMATIC) FROM DESULVOBRIO VULGARIS HILDENBOROUGH (NATIVE)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 18 residues within 4Å: Chain A: P.91, H.96, L.99, E.100, H.103, H.158, P.159, I.162 Chain D: P.91, E.93, F.95, H.96, L.99, L.119, H.158, P.159, A.160 Ligands: HEM.58 18 PLIP interactions: 8 interactions with chain A, 10 interactions with chain D, Hydrophobic interactions: A:P.91, A:L.99, A:L.99, A:P.159, A:P.159, A:I.162, D:P.91, D:P.91, D:F.95, D:L.99, D:L.119, D:P.159, D:P.159 Salt bridges: A:H.103, D:H.96, D:H.158 Metal complexes: A:H.96, D:H.96 HEM.20: 18 residues within 4Å: Chain B: P.91, H.96, L.99, E.100, H.103, H.158, P.159, I.162 Chain C: P.91, E.93, F.95, H.96, L.99, L.119, H.158, P.159, A.160 Ligands: HEM.39 18 PLIP interactions: 10 interactions with chain C, 8 interactions with chain B, Hydrophobic interactions: C:P.91, C:P.91, C:F.95, C:L.99, C:L.119, C:P.159, C:P.159, B:P.91, B:L.99, B:L.99, B:P.159, B:P.159, B:I.162 Salt bridges: C:H.96, C:H.158, B:H.103 Metal complexes: C:H.96, B:H.96 HEM.39: 18 residues within 4Å: Chain B: P.91, E.93, F.95, H.96, L.99, L.119, H.158, P.159, A.160 Chain C: P.91, H.96, L.99, E.100, H.103, H.158, P.159, I.162 Ligands: HEM.20 18 PLIP interactions: 10 interactions with chain B, 8 interactions with chain C, Hydrophobic interactions: B:P.91, B:P.91, B:F.95, B:L.99, B:L.119, B:P.159, B:P.159, C:P.91, C:L.99, C:L.99, C:P.159, C:P.159, C:I.162 Salt bridges: B:H.96, B:H.158, C:H.103 Metal complexes: B:H.96, C:H.96 HEM.58: 18 residues within 4Å: Chain A: P.91, E.93, F.95, H.96, L.99, L.119, H.158, P.159, A.160 Chain D: P.91, H.96, L.99, E.100, H.103, H.158, P.159, I.162 Ligands: HEM.1 18 PLIP interactions: 10 interactions with chain A, 8 interactions with chain D, Hydrophobic interactions: A:P.91, A:P.91, A:F.95, A:L.99, A:L.119, A:P.159, A:P.159, D:P.91, D:L.99, D:L.99, D:P.159, D:P.159, D:I.162 Salt bridges: A:H.96, A:H.158, D:H.103 Metal complexes: A:H.96, D:H.96

20 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 6 residues within 4Å: Chain A: I.90, G.92, E.93, E.94, T.156, H.158 Ligand excluded by PLIP SO4.3: 6 residues within 4Å: Chain A: H.103, R.114, V.115, S.116, V.117, R.267 Ligand excluded by PLIP SO4.4: 8 residues within 4Å: Chain A: F.17, L.87, H.88, T.89, H.154, M.210, A.211 Ligands: NA.19 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: P.43, V.44, R.45 Ligand excluded by PLIP SO4.6: 7 residues within 4Å: Chain A: T.19, S.20, V.21, I.53, G.214, D.215 Ligands: GOL.15 Ligand excluded by PLIP SO4.21: 6 residues within 4Å: Chain B: I.90, G.92, E.93, E.94, T.156, H.158 Ligand excluded by PLIP SO4.22: 6 residues within 4Å: Chain B: H.103, R.114, V.115, S.116, V.117, R.267 Ligand excluded by PLIP SO4.23: 8 residues within 4Å: Chain B: F.17, L.87, H.88, T.89, H.154, M.210, A.211 Ligands: NA.38 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain B: P.43, V.44, R.45 Ligand excluded by PLIP SO4.25: 7 residues within 4Å: Chain B: T.19, S.20, V.21, I.53, G.214, D.215 Ligands: GOL.34 Ligand excluded by PLIP SO4.40: 6 residues within 4Å: Chain C: I.90, G.92, E.93, E.94, T.156, H.158 Ligand excluded by PLIP SO4.41: 6 residues within 4Å: Chain C: H.103, R.114, V.115, S.116, V.117, R.267 Ligand excluded by PLIP SO4.42: 8 residues within 4Å: Chain C: F.17, L.87, H.88, T.89, H.154, M.210, A.211 Ligands: NA.57 Ligand excluded by PLIP SO4.43: 3 residues within 4Å: Chain C: P.43, V.44, R.45 Ligand excluded by PLIP SO4.44: 7 residues within 4Å: Chain C: T.19, S.20, V.21, I.53, G.214, D.215 Ligands: GOL.53 Ligand excluded by PLIP SO4.59: 6 residues within 4Å: Chain D: I.90, G.92, E.93, E.94, T.156, H.158 Ligand excluded by PLIP SO4.60: 6 residues within 4Å: Chain D: H.103, R.114, V.115, S.116, V.117, R.267 Ligand excluded by PLIP SO4.61: 8 residues within 4Å: Chain D: F.17, L.87, H.88, T.89, H.154, M.210, A.211 Ligands: NA.76 Ligand excluded by PLIP SO4.62: 3 residues within 4Å: Chain D: P.43, V.44, R.45 Ligand excluded by PLIP SO4.63: 7 residues within 4Å: Chain D: T.19, S.20, V.21, I.53, G.214, D.215 Ligands: GOL.72 Ligand excluded by PLIP

40 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: V.136, R.143, L.174, D.175, L.178 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain A: T.49, A.50, K.51, M.52 Ligand excluded by PLIP GOL.9: 2 residues within 4Å: Chain A: K.144, R.203 Ligand excluded by PLIP GOL.10: 3 residues within 4Å: Chain A: K.202, R.203, E.239 Ligand excluded by PLIP GOL.11: 3 residues within 4Å: Chain A: P.65, E.69 Ligands: GOL.49 Ligand excluded by PLIP GOL.12: 3 residues within 4Å: Chain A: D.197, V.198, K.200 Ligand excluded by PLIP GOL.13: 5 residues within 4Å: Chain A: S.138, E.249, S.250, D.251, A.252 Ligand excluded by PLIP GOL.14: 4 residues within 4Å: Chain A: W.172, P.176, R.199 Ligands: GOL.71 Ligand excluded by PLIP GOL.15: 7 residues within 4Å: Chain A: F.17, H.154, M.210, G.214, D.215, H.216 Ligands: SO4.6 Ligand excluded by PLIP GOL.16: 4 residues within 4Å: Chain A: R.58, G.61, I.62, A.63 Ligand excluded by PLIP GOL.26: 5 residues within 4Å: Chain B: V.136, R.143, L.174, D.175, L.178 Ligand excluded by PLIP GOL.27: 4 residues within 4Å: Chain B: T.49, A.50, K.51, M.52 Ligand excluded by PLIP GOL.28: 2 residues within 4Å: Chain B: K.144, R.203 Ligand excluded by PLIP GOL.29: 3 residues within 4Å: Chain B: K.202, R.203, E.239 Ligand excluded by PLIP GOL.30: 3 residues within 4Å: Chain B: P.65, E.69 Ligands: GOL.68 Ligand excluded by PLIP GOL.31: 3 residues within 4Å: Chain B: D.197, V.198, K.200 Ligand excluded by PLIP GOL.32: 5 residues within 4Å: Chain B: S.138, E.249, S.250, D.251, A.252 Ligand excluded by PLIP GOL.33: 4 residues within 4Å: Chain B: W.172, P.176, R.199 Ligands: GOL.52 Ligand excluded by PLIP GOL.34: 7 residues within 4Å: Chain B: F.17, H.154, M.210, G.214, D.215, H.216 Ligands: SO4.25 Ligand excluded by PLIP GOL.35: 4 residues within 4Å: Chain B: R.58, G.61, I.62, A.63 Ligand excluded by PLIP GOL.45: 5 residues within 4Å: Chain C: V.136, R.143, L.174, D.175, L.178 Ligand excluded by PLIP GOL.46: 4 residues within 4Å: Chain C: T.49, A.50, K.51, M.52 Ligand excluded by PLIP GOL.47: 2 residues within 4Å: Chain C: K.144, R.203 Ligand excluded by PLIP GOL.48: 3 residues within 4Å: Chain C: K.202, R.203, E.239 Ligand excluded by PLIP GOL.49: 3 residues within 4Å: Chain C: P.65, E.69 Ligands: GOL.11 Ligand excluded by PLIP GOL.50: 3 residues within 4Å: Chain C: D.197, V.198, K.200 Ligand excluded by PLIP GOL.51: 5 residues within 4Å: Chain C: S.138, E.249, S.250, D.251, A.252 Ligand excluded by PLIP GOL.52: 4 residues within 4Å: Chain C: W.172, P.176, R.199 Ligands: GOL.33 Ligand excluded by PLIP GOL.53: 7 residues within 4Å: Chain C: F.17, H.154, M.210, G.214, D.215, H.216 Ligands: SO4.44 Ligand excluded by PLIP GOL.54: 4 residues within 4Å: Chain C: R.58, G.61, I.62, A.63 Ligand excluded by PLIP GOL.64: 5 residues within 4Å: Chain D: V.136, R.143, L.174, D.175, L.178 Ligand excluded by PLIP GOL.65: 4 residues within 4Å: Chain D: T.49, A.50, K.51, M.52 Ligand excluded by PLIP GOL.66: 2 residues within 4Å: Chain D: K.144, R.203 Ligand excluded by PLIP GOL.67: 3 residues within 4Å: Chain D: K.202, R.203, E.239 Ligand excluded by PLIP GOL.68: 3 residues within 4Å: Chain D: P.65, E.69 Ligands: GOL.30 Ligand excluded by PLIP GOL.69: 3 residues within 4Å: Chain D: D.197, V.198, K.200 Ligand excluded by PLIP GOL.70: 5 residues within 4Å: Chain D: S.138, E.249, S.250, D.251, A.252 Ligand excluded by PLIP GOL.71: 4 residues within 4Å: Chain D: W.172, P.176, R.199 Ligands: GOL.14 Ligand excluded by PLIP GOL.72: 7 residues within 4Å: Chain D: F.17, H.154, M.210, G.214, D.215, H.216 Ligands: SO4.63 Ligand excluded by PLIP GOL.73: 4 residues within 4Å: Chain D: R.58, G.61, I.62, A.63 Ligand excluded by PLIP

4 x CO2: CARBON DIOXIDE(Non-covalent)

CO2.17: 3 residues within 4Å: Chain A: F.17, E.184, H.216 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.154, A:H.216 CO2.36: 3 residues within 4Å: Chain B: F.17, E.184, H.216 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.216 CO2.55: 3 residues within 4Å: Chain C: F.17, E.184, H.216 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.154, C:H.216 CO2.74: 3 residues within 4Å: Chain D: F.17, E.184, H.216 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.216

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

CL.18: 2 residues within 4Å: Chain A: P.140, A.141 Ligand excluded by PLIP CL.37: 2 residues within 4Å: Chain B: P.140, A.141 Ligand excluded by PLIP CL.56: 2 residues within 4Å: Chain C: P.140, A.141 Ligand excluded by PLIP CL.75: 2 residues within 4Å: Chain D: P.140, A.141 Ligand excluded by PLIP

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

NA.19: 6 residues within 4Å: Chain A: T.89, G.153, H.154, Y.164, M.210 Ligands: SO4.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.89, A:T.89, A:H.154 NA.38: 6 residues within 4Å: Chain B: T.89, G.153, H.154, Y.164, M.210 Ligands: SO4.23 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.89, B:H.154, B:Y.164 NA.57: 6 residues within 4Å: Chain C: T.89, G.153, H.154, Y.164, M.210 Ligands: SO4.42 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.89, C:T.89, C:H.154 NA.76: 6 residues within 4Å: Chain D: T.89, G.153, H.154, Y.164, M.210 Ligands: SO4.61 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.89, D:H.154, D:Y.164

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Romao, C.V. et al., Evolution in a Family of Chelatases Facilitated by the Introduction of Active Site Asymmetry and Protein Oligomerization. Proc.Natl.Acad.Sci.USA (2011)

Release Date

2010-12-22

Peptides

CHELATASE, PUTATIVE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

CHELATASE, PUTATIVE

Related Entries With Identical Sequence