SMTL ID : 2p4g.1

CRYSTAL STRUCTURE OF A PYRIMIDINE REDUCTASE-LIKE PROTEIN (DIP1392) FROM CORYNEBACTERIUM DIPHTHERIAE NCTC AT 2.30 A RESOLUTION

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x NO3: NITRATE ION(Non-functional Binders)

NO3.1: 7 residues within 4Å: Chain A: P.56, M.57, G.58, D.59, N.251, L.253 Chain B: R.240 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.240, A:N.251 NO3.17: 7 residues within 4Å: Chain A: R.240 Chain B: P.56, M.57, G.58, D.59, N.251, L.253 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.240, B:N.251

30 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 4 residues within 4Å: Chain A: R.70, E.86, Y.88 Ligands: EDO.6 Ligand excluded by PLIP EDO.3: 7 residues within 4Å: Chain A: G.79, T.82, G.196, P.197, S.198, V.199 Ligands: EDO.13 Ligand excluded by PLIP EDO.4: 3 residues within 4Å: Chain A: P.90, S.125, E.126 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: L.243, E.244, M.245, L.246 Chain B: S.248 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: R.70, Y.88, G.89, P.90 Ligands: EDO.2 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: A.80, A.83, R.84, L.114, F.121, F.128 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: C.107, L.109, P.110, K.111, E.135 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain A: I.39, A.40, I.41, D.62, E.194, Y.200 Ligands: EDO.11 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: Y.23, G.71, I.97, Q.100, R.101, R.106 Ligand excluded by PLIP EDO.11: 9 residues within 4Å: Chain A: A.40, I.41, A.48, S.54, G.196, P.197, Y.200 Ligands: EDO.9, EDO.15 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: L.119, Y.120, F.121, F.123, R.155, K.158 Ligand excluded by PLIP EDO.13: 7 residues within 4Å: Chain A: G.79, A.80, E.81, L.115, S.116, K.117 Ligands: EDO.3 Ligand excluded by PLIP EDO.14: 1 residues within 4Å: Chain A: D.131 Ligand excluded by PLIP EDO.15: 7 residues within 4Å: Chain A: T.49, S.54, T.82, K.85, E.86, P.197 Ligands: EDO.11 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain A: K.111, S.134, S.137, G.163 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain B: R.70, E.86, Y.88 Ligands: EDO.22 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain B: G.79, T.82, G.196, P.197, S.198, V.199 Ligands: EDO.29 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain B: P.90, S.125, E.126 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain A: S.248 Chain B: L.243, E.244, M.245, L.246 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain B: R.70, Y.88, G.89, P.90 Ligands: EDO.18 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain B: A.80, A.83, R.84, L.114, F.121, F.128 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain B: C.107, L.109, P.110, K.111, E.135 Ligand excluded by PLIP EDO.25: 7 residues within 4Å: Chain B: I.39, A.40, I.41, D.62, E.194, Y.200 Ligands: EDO.27 Ligand excluded by PLIP EDO.26: 6 residues within 4Å: Chain B: Y.23, G.71, I.97, Q.100, R.101, R.106 Ligand excluded by PLIP EDO.27: 9 residues within 4Å: Chain B: A.40, I.41, A.48, S.54, G.196, P.197, Y.200 Ligands: EDO.25, EDO.31 Ligand excluded by PLIP EDO.28: 6 residues within 4Å: Chain B: L.119, Y.120, F.121, F.123, R.155, K.158 Ligand excluded by PLIP EDO.29: 7 residues within 4Å: Chain B: G.79, A.80, E.81, L.115, S.116, K.117 Ligands: EDO.19 Ligand excluded by PLIP EDO.30: 1 residues within 4Å: Chain B: D.131 Ligand excluded by PLIP EDO.31: 7 residues within 4Å: Chain B: T.49, S.54, T.82, K.85, E.86, P.197 Ligands: EDO.27 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain B: K.111, S.134, S.137, G.163 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of hypothetical protein (NP_939744.1) from Corynebacterium diphtheriae at 2.30 A resolution. To be published

Release Date

2007-03-27

Peptides

Hypothetical protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Hypothetical protein