SMTL ID : 1vq2.2 (1 other biounit)

CRYSTAL STRUCTURE OF T4-BACTERIOPHAGE DEOXYCYTIDYLATE DEAMINASE, MUTANT R115E

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.104, C.132, C.135 Ligands: DDN.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.104, A:C.132, A:C.135 ZN.2: 6 residues within 4Å: Chain A: C.19, C.20, C.49, H.94, E.102 Ligands: DDN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.19, A:C.49, A:H.94, A:E.102 ZN.4: 4 residues within 4Å: Chain B: H.104, C.132, C.135 Ligands: DDN.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.104, B:C.132, B:C.135 ZN.5: 6 residues within 4Å: Chain B: C.19, C.20, C.49, H.94, E.102 Ligands: DDN.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.19, B:C.49, B:H.94, B:E.102 ZN.7: 4 residues within 4Å: Chain C: H.104, C.132, C.135 Ligands: DDN.9 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.104, C:C.132, C:C.135 ZN.8: 6 residues within 4Å: Chain C: C.19, C.20, C.49, H.94, E.102 Ligands: DDN.9 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.19, C:C.49, C:H.94, C:E.102 ZN.10: 4 residues within 4Å: Chain D: H.104, C.132, C.135 Ligands: DDN.12 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.104, D:C.132, D:C.135 ZN.11: 6 residues within 4Å: Chain D: C.19, C.20, C.49, H.94, E.102 Ligands: DDN.12 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.19, D:C.49, D:H.94, D:E.102 ZN.13: 4 residues within 4Å: Chain E: H.104, C.132, C.135 Ligands: DDN.15 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.104, E:C.132, E:C.135 ZN.14: 6 residues within 4Å: Chain E: C.19, C.20, C.49, H.94, E.102 Ligands: DDN.15 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.19, E:C.49, E:H.94, E:E.102 ZN.16: 4 residues within 4Å: Chain F: H.104, C.132, C.135 Ligands: DDN.18 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.104, F:C.132, F:C.135 ZN.17: 6 residues within 4Å: Chain F: C.19, C.20, C.49, H.94, E.102 Ligands: DDN.18 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.19, F:C.49, F:H.94, F:E.102

6 x DDN: 3,4-DIHYDRO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE(Non-covalent)

DDN.3: 20 residues within 4Å: Chain A: C.19, S.21, W.22, V.24, N.40, R.91, H.94, S.95, S.98, E.102, H.104, A.105, E.106, P.131, C.132, C.135, Y.153, K.155 Ligands: ZN.1, ZN.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.153 Hydrogen bonds: A:S.21, A:N.40, A:S.95, A:S.95, A:S.98, A:A.105, A:E.106, A:C.132, A:Y.153 Salt bridges: A:R.91, A:H.94 DDN.6: 20 residues within 4Å: Chain B: C.19, S.21, W.22, V.24, N.40, R.91, H.94, S.95, S.98, E.102, H.104, A.105, E.106, P.131, C.132, C.135, Y.153, K.155 Ligands: ZN.4, ZN.5 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.153 Hydrogen bonds: B:S.21, B:N.40, B:S.95, B:S.95, B:S.98, B:A.105, B:E.106, B:C.132, B:Y.153 Salt bridges: B:R.91, B:H.94 DDN.9: 20 residues within 4Å: Chain C: C.19, S.21, W.22, V.24, N.40, R.91, H.94, S.95, S.98, E.102, H.104, A.105, E.106, P.131, C.132, C.135, Y.153, K.155 Ligands: ZN.7, ZN.8 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:Y.153 Hydrogen bonds: C:S.21, C:N.40, C:S.95, C:S.95, C:S.98, C:A.105, C:E.106, C:C.132, C:Y.153 Salt bridges: C:R.91, C:H.94 DDN.12: 20 residues within 4Å: Chain D: C.19, S.21, W.22, V.24, N.40, R.91, H.94, S.95, S.98, E.102, H.104, A.105, E.106, P.131, C.132, C.135, Y.153, K.155 Ligands: ZN.10, ZN.11 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:Y.153 Hydrogen bonds: D:S.21, D:N.40, D:S.95, D:S.95, D:S.98, D:A.105, D:E.106, D:C.132 Salt bridges: D:R.91, D:H.94 DDN.15: 20 residues within 4Å: Chain E: C.19, S.21, W.22, V.24, N.40, R.91, H.94, S.95, S.98, E.102, H.104, A.105, E.106, P.131, C.132, C.135, Y.153, K.155 Ligands: ZN.13, ZN.14 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:Y.153 Hydrogen bonds: E:S.21, E:N.40, E:S.95, E:S.95, E:S.98, E:A.105, E:E.106, E:C.132 Salt bridges: E:R.91, E:H.94 DDN.18: 20 residues within 4Å: Chain F: C.19, S.21, W.22, V.24, N.40, R.91, H.94, S.95, S.98, E.102, H.104, A.105, E.106, P.131, C.132, C.135, Y.153, K.155 Ligands: ZN.16, ZN.17 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:Y.153 Hydrogen bonds: F:S.21, F:N.40, F:S.95, F:S.95, F:S.98, F:A.105, F:E.106, F:C.132 Salt bridges: F:R.91, F:H.94

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Almog, R. et al., Three-Dimensional Structure of the R115E Mutant of T4-Bacteriophage 2'-Deoxycytidylate Deaminase. Biochemistry (2004)

Release Date

2004-12-21

Peptides

DEOXYCYTIDYLATE DEAMINASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

DEOXYCYTIDYLATE DEAMINASE

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