SMTL ID : 3ram.1

Crystal structure of HmrA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

9 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: C.93, E.128, E.129, H.341 Ligands: ZN.2, GOL.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.93, A:E.129, A:E.129, A:H.341 ZN.2: 7 residues within 4Å: Chain A: C.93, H.95, E.128, E.129, H.156 Ligands: ZN.1, GOL.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.93, A:H.95, A:H.156 ZN.12: 6 residues within 4Å: Chain B: C.93, E.128, E.129, H.341 Ligands: ZN.13, GOL.22 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.93, B:E.129, B:E.129, B:H.341 ZN.13: 7 residues within 4Å: Chain B: C.93, H.95, E.128, E.129, H.156 Ligands: ZN.12, GOL.22 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.93, B:H.95, B:H.156 ZN.24: 1 residues within 4Å: Chain B: H.388 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.388 ZN.25: 5 residues within 4Å: Chain C: C.93, E.129, H.341 Ligands: ZN.26, GOL.33 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.93, C:E.129, C:E.129, C:H.341 ZN.26: 7 residues within 4Å: Chain C: C.93, H.95, E.128, E.129, H.156 Ligands: ZN.25, GOL.33 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.93, C:H.95, C:H.156 ZN.34: 6 residues within 4Å: Chain D: C.93, E.128, E.129, H.341 Ligands: ZN.35, GOL.37 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.93, D:E.129, D:E.129, D:H.341 ZN.35: 7 residues within 4Å: Chain D: C.93, H.95, E.128, E.129, H.156 Ligands: ZN.34, GOL.37 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.93, D:H.95, D:H.156

32 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: I.43, D.44, K.47 Ligand excluded by PLIP GOL.4: 5 residues within 4Å: Chain A: D.50, E.52, T.67, Y.68, D.69 Ligand excluded by PLIP GOL.5: 10 residues within 4Å: Chain A: C.93, E.128, E.129, H.156, S.314, H.328 Ligands: ZN.1, ZN.2, GOL.6, GOL.8 Ligand excluded by PLIP GOL.6: 7 residues within 4Å: Chain A: C.93, H.156, P.157, Y.162, H.330, G.340 Ligands: GOL.5 Ligand excluded by PLIP GOL.7: 7 residues within 4Å: Chain A: H.219, Y.241, S.314 Chain B: H.183, S.185, N.230 Ligands: GOL.8 Ligand excluded by PLIP GOL.8: 12 residues within 4Å: Chain A: E.128, E.129, G.130, S.135, V.170, Q.278, V.281, S.314, T.315, D.316 Ligands: GOL.5, GOL.7 Ligand excluded by PLIP GOL.9: 9 residues within 4Å: Chain A: S.181, D.224, G.226, K.227, A.228, I.231, P.233, D.234, Y.235 Ligand excluded by PLIP GOL.10: 4 residues within 4Å: Chain A: N.258, Y.272, E.273, F.274 Ligand excluded by PLIP GOL.11: 3 residues within 4Å: Chain A: I.266, C.270, D.271 Ligand excluded by PLIP GOL.14: 7 residues within 4Å: Chain B: C.93, H.156, G.158, Y.162, H.330, G.340 Ligands: GOL.22 Ligand excluded by PLIP GOL.15: 8 residues within 4Å: Chain B: I.36, S.39, R.40, I.43, T.55, A.61, T.62, G.63 Ligand excluded by PLIP GOL.16: 8 residues within 4Å: Chain A: V.221 Chain B: S.181, G.226, K.227, A.228, I.231, P.233, D.234 Ligand excluded by PLIP GOL.17: 10 residues within 4Å: Chain A: R.217 Chain B: A.184, S.185, E.186, N.187, A.188, D.189 Chain D: Q.210, I.212, K.214 Ligand excluded by PLIP GOL.18: 7 residues within 4Å: Chain A: F.202, R.209, G.220 Chain B: N.193, D.196, I.232 Chain D: Q.210 Ligand excluded by PLIP GOL.19: 4 residues within 4Å: Chain B: N.258, Y.272, E.273, F.274 Ligand excluded by PLIP GOL.20: 4 residues within 4Å: Chain B: K.332, G.334, S.335, H.353 Ligand excluded by PLIP GOL.21: 3 residues within 4Å: Chain B: N.133, P.276, N.279 Ligand excluded by PLIP GOL.22: 9 residues within 4Å: Chain B: C.93, E.128, E.129, H.156, G.313, S.314 Ligands: ZN.12, ZN.13, GOL.14 Ligand excluded by PLIP GOL.23: 1 residues within 4Å: Chain B: Y.178 Ligand excluded by PLIP GOL.27: 7 residues within 4Å: Chain C: C.93, H.156, G.158, H.330, G.340, F.345 Ligands: GOL.33 Ligand excluded by PLIP GOL.28: 8 residues within 4Å: Chain A: G.204, Q.207, H.211 Chain C: L.192, N.193, D.196, Q.267, T.268 Ligand excluded by PLIP GOL.29: 9 residues within 4Å: Chain A: Q.210, I.212, K.214 Chain C: A.184, S.185, E.186, N.187, A.188 Chain D: R.217 Ligand excluded by PLIP GOL.30: 4 residues within 4Å: Chain C: E.255, N.258, F.274 Ligands: GOL.31 Ligand excluded by PLIP GOL.31: 6 residues within 4Å: Chain C: N.258, Y.272, E.273, F.274 Ligands: GOL.30, GOL.32 Ligand excluded by PLIP GOL.32: 6 residues within 4Å: Chain C: D.174, K.176, E.273, G.275, P.276 Ligands: GOL.31 Ligand excluded by PLIP GOL.33: 8 residues within 4Å: Chain C: C.93, E.128, E.129, G.313, S.314 Ligands: ZN.25, ZN.26, GOL.27 Ligand excluded by PLIP GOL.36: 3 residues within 4Å: Chain D: K.47, I.53, T.55 Ligand excluded by PLIP GOL.37: 10 residues within 4Å: Chain D: C.93, E.128, E.129, H.156, G.313, S.314 Ligands: ZN.34, ZN.35, GOL.39, GOL.40 Ligand excluded by PLIP GOL.38: 8 residues within 4Å: Chain B: Q.210 Chain C: F.202, R.209, H.219, G.220 Chain D: N.193, D.196, I.232 Ligand excluded by PLIP GOL.39: 7 residues within 4Å: Chain D: H.156, P.157, G.158, H.330, G.340, F.345 Ligands: GOL.37 Ligand excluded by PLIP GOL.40: 10 residues within 4Å: Chain D: E.128, E.129, G.130, V.172, Y.241, Q.278, V.281, S.314, T.315 Ligands: GOL.37 Ligand excluded by PLIP GOL.41: 3 residues within 4Å: Chain D: H.26, E.27, R.346 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Botelho, T.O. et al., Structural and Functional Analyses Reveal That Staphylococcus aureus Antibiotic Resistance Factor HmrA Is a Zinc-dependent Endopeptidase. J.Biol.Chem. (2011)

Release Date

2011-05-25

Peptides

HmrA protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

HmrA protein