SMTL ID : 3h5r.1

Crystal structure of E. coli MccB + Succinimide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x MET- ARG- THR- GLY- ASN- ALA- SNN: Microcin C7 analog(Non-covalent)

MET-ARG-THR-GLY-ASN-ALA-SNN.1: 22 residues within 4Å: Chain A: I.129, S.215, A.216, D.217, N.239, A.240, G.241, Y.242, V.243, V.248, Y.261, P.291, R.325, G.327, W.329, H.336, Q.338 Chain B: K.13, Y.17, L.22, E.29, Y.31 19 PLIP interactions: 7 interactions with chain B, 12 interactions with chain A Hydrophobic interactions: B:L.22, A:Y.242, A:P.291 Hydrogen bonds: B:K.13, B:K.13, B:Y.17, B:E.29, B:E.29, B:E.29, A:N.239, A:A.240, A:Y.242, A:Y.242, A:R.325, A:R.325, A:Q.338 Water bridges: A:I.129, A:A.216, A:D.217 MET-ARG-THR-GLY-ASN-ALA-SNN.2: 23 residues within 4Å: Chain A: K.13, Y.17, L.22, E.29, Y.31 Chain B: I.129, S.215, A.216, D.217, N.239, A.240, G.241, Y.242, V.243, V.248, Y.261, P.291, R.325, I.326, G.327, W.329, H.336, Q.338 20 PLIP interactions: 8 interactions with chain A, 12 interactions with chain B Hydrophobic interactions: A:K.13, A:L.22, B:D.217, B:P.291 Hydrogen bonds: A:K.13, A:Y.17, A:E.29, A:E.29, B:D.217, B:N.239, B:A.240, B:Y.242, B:Y.242, B:R.325, B:R.325, B:Q.338 Water bridges: A:G.26, A:E.29, B:N.239, B:R.325 MET-ARG-THR-GLY-ASN-ALA-SNN.3: 7 residues within 4Å: Chain C: V.243, I.246, R.325, G.327, H.336, Q.338 Chain D: E.29 Protein-ligand interaction information (PLIP) not available MET-ARG-THR-GLY-ASN-ALA-SNN.4: 8 residues within 4Å: Chain C: E.29 Chain D: V.243, I.246, R.325, G.327, W.329, H.336, Q.338 Protein-ligand interaction information (PLIP) not available

4 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain A: C.260, C.263, C.346, C.349 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.260, A:C.263, A:C.346, A:C.349 ZN.6: 4 residues within 4Å: Chain B: C.260, C.263, C.346, C.349 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.260, B:C.263, B:C.346, B:C.349 ZN.8: 4 residues within 4Å: Chain C: C.260, C.263, C.346, C.349 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.260, C:C.263, C:C.346, C:C.349 ZN.10: 4 residues within 4Å: Chain D: C.260, C.263, C.346, C.349 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.260, D:C.263, D:C.346, D:C.349

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

SO4.7: 2 residues within 4Å: Chain A: N.62 Chain B: K.281 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.62 Salt bridges: B:K.281 SO4.9: 3 residues within 4Å: Chain C: N.62 Chain D: N.277, K.281 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:N.277 Salt bridges: D:K.281 Water bridges: C:T.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Regni, C.A. et al., How the MccB bacterial ancestor of ubiquitin E1 initiates biosynthesis of the microcin C7 antibiotic. Embo J. (2009)

Release Date

2009-06-16

Peptides

MccB protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

MccB protein

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