SMTL ID : 2qyv.1

Crystal structure of putative Xaa-His dipeptidase (YP_718209.1) from Haemophilus somnus 129PT at 2.11 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.77, D.116, E.146, D.170 Ligands: ZN.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.77, A:D.116, A:D.170, A:D.170 ZN.2: 4 residues within 4Å: Chain A: D.116, E.147, H.459 Ligands: ZN.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.116, A:E.147, A:E.147, A:H.459 ZN.21: 5 residues within 4Å: Chain B: H.77, D.116, E.146, D.170 Ligands: ZN.22 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.77, B:D.116, B:D.170, B:D.170 ZN.22: 4 residues within 4Å: Chain B: D.116, E.147, H.459 Ligands: ZN.21 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.116, B:E.147, B:E.147

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

SO4.3: 6 residues within 4Å: Chain A: H.215, N.259, R.367, A.432, G.433, H.459 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: Q.9, P.10, K.11 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: N.68, R.69, S.486 Ligand excluded by PLIP SO4.6: 5 residues within 4Å: Chain A: G.255, S.256, P.262, R.263, E.264 Ligand excluded by PLIP SO4.7: 4 residues within 4Å: Chain A: N.174, T.454, H.466, A.469 Ligand excluded by PLIP SO4.8: 2 residues within 4Å: Chain A: S.395, G.396 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain A: E.201, H.202, K.306, K.309 Ligand excluded by PLIP SO4.10: 1 residues within 4Å: Chain A: K.284 Ligand excluded by PLIP SO4.23: 7 residues within 4Å: Chain B: H.215, N.259, R.367, Y.398, A.432, G.433, H.459 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain B: Q.9, P.10, K.11, E.471 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain B: N.68, R.69, S.486 Ligand excluded by PLIP SO4.26: 5 residues within 4Å: Chain B: G.255, S.256, P.262, R.263, E.264 Ligand excluded by PLIP SO4.27: 2 residues within 4Å: Chain B: S.395, G.396 Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain B: E.201, H.202, K.306, K.309 Ligand excluded by PLIP SO4.29: 4 residues within 4Å: Chain B: N.174, T.454, H.466, A.469 Ligand excluded by PLIP SO4.30: 1 residues within 4Å: Chain B: K.284 Ligand excluded by PLIP SO4.31: 2 residues within 4Å: Chain B: D.357, N.358 Ligand excluded by PLIP SO4.32: 1 residues within 4Å: Chain B: N.199 Ligand excluded by PLIP

17 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 6 residues within 4Å: Chain A: R.233, E.237, F.285 Chain B: S.372, S.375, Y.376 Ligand excluded by PLIP GOL.12: 4 residues within 4Å: Chain A: Q.239, Q.317, K.320 Chain B: S.386 Ligand excluded by PLIP GOL.13: 7 residues within 4Å: Chain A: L.12, Q.15, W.16, Q.19, F.36, W.40, E.129 Ligand excluded by PLIP GOL.14: 7 residues within 4Å: Chain A: P.192, E.194, Q.317, C.318, N.321, A.388, Q.389 Ligand excluded by PLIP GOL.15: 6 residues within 4Å: Chain A: F.46, F.47, R.59, K.60, P.61, R.162 Ligand excluded by PLIP GOL.16: 3 residues within 4Å: Chain A: S.386 Chain B: Q.239, K.320 Ligand excluded by PLIP GOL.17: 8 residues within 4Å: Chain A: K.229, N.327, V.328, L.329, P.330, N.331 Chain B: Y.376 Ligands: GOL.37 Ligand excluded by PLIP GOL.18: 5 residues within 4Å: Chain A: R.233, I.289, L.293 Chain B: R.335, Y.376 Ligand excluded by PLIP GOL.33: 6 residues within 4Å: Chain A: S.372, S.375, Y.376 Chain B: R.233, E.237, F.285 Ligand excluded by PLIP GOL.34: 4 residues within 4Å: Chain B: K.382, I.392, N.393, L.394 Ligand excluded by PLIP GOL.35: 4 residues within 4Å: Chain B: L.12, Q.15, W.16, E.129 Ligand excluded by PLIP GOL.36: 7 residues within 4Å: Chain A: R.335, Y.376 Chain B: V.230, R.233, I.289, E.292, L.293 Ligand excluded by PLIP GOL.37: 9 residues within 4Å: Chain A: Y.376, L.380 Chain B: K.229, N.327, V.328, L.329, P.330, N.331 Ligands: GOL.17 Ligand excluded by PLIP GOL.38: 6 residues within 4Å: Chain B: G.45, F.46, F.47, R.59, K.60, P.61 Ligand excluded by PLIP GOL.39: 3 residues within 4Å: Chain B: R.148, N.186, R.258 Ligand excluded by PLIP GOL.40: 3 residues within 4Å: Chain B: Q.279, S.280, Q.283 Ligand excluded by PLIP GOL.41: 7 residues within 4Å: Chain B: Q.239, F.245, F.247, T.248, S.316, T.319, K.320 Ligand excluded by PLIP

3 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.19: 2 residues within 4Å: Chain A: Q.279, Q.283 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.279, A:Q.283 IPA.20: 2 residues within 4Å: Chain A: E.308, K.309 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.309 Water bridges: A:V.307 IPA.42: 2 residues within 4Å: Chain B: E.308, K.309 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:K.309

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of putative Xaa-His dipeptidase (YP_718209.1) from Haemophilus somnus 129PT at 2.11 A resolution. To be published

Release Date

2007-08-28

Peptides

Xaa-His dipeptidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Xaa-His dipeptidase