MolNFT v1 · #142282 · protein
Crystal structure of photosystem II from an sqdg-deficient mutant of thermosynechococcus elongatus
5ZZN: “Crystal structure of photosystem II from an sqdg-deficient mutant of thermosynechococcus elongatus”. X-ray diffraction, 17 ligands (CLA, UNL, BCR). MolNFT v1 #142282 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ZZN
- Type
- protein
- Length
- 5,253 residues
- Chains
- 38
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- UniProt
- P0A444, Q8DIQ1, Q8DIF8, Q8CM25, Q8DIP0, Q8DIN9, Q8DJ43, Q8DJZ6, P59087, Q9F1K9, Q8DIN8, Q8DHA7, P0A431, Q8DIQ0, Q9F1L5, P0A386, Q8DJI1, Q9F1R6, Q8DHJ2
- Ligands
- CLA, UNL, BCR, LHG, LMG, DGD, PHO, PL9, OEX, BCT, HEM, RRX, HEC, CA, MG, FE2, CL
Structure
x-ray diffraction · 28 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, a | — | protein | 334 | — | P0A444 |
| B | — | protein | 505 | — | Q8DIQ1 |
| C | — | protein | 451 | — | Q8DIF8 |
| D, d | — | protein | 342 | — | Q8CM25 |
| E | — | protein | 80 | — | Q8DIP0 |
| F | — | protein | 34 | — | Q8DIN9 |
| H, h | — | protein | 63 | — | Q8DJ43 |
| I | — | protein | 35 | — | Q8DJZ6 |
| J | — | protein | 37 | — | P59087 |
| K, k | — | protein | 37 | — | Q9F1K9 |
| L | — | protein | 36 | — | Q8DIN8 |
| M | — | protein | 33 | — | Q8DHA7 |
| O, o | — | protein | 243 | — | P0A431 |
| T, t | — | protein | 30 | — | Q8DIQ0 |
| U, u | — | protein | 97 | — | Q9F1L5 |
| V, v | — | protein | 137 | — | P0A386 |
| Y, y | — | protein | 29 | — | Q8DJI1 |
| X | — | protein | 39 | — | Q9F1R6 |
| Z, z | — | protein | 62 | — | Q8DHJ2 |
| b | — | protein | 504 | — | Q8DIQ1 |
| c | — | protein | 455 | — | Q8DIF8 |
| e | — | protein | 81 | — | Q8DIP0 |
| f | — | protein | 32 | — | Q8DIN9 |
| i | — | protein | 36 | — | Q8DJZ6 |
| j | — | protein | 40 | — | P59087 |
| l | — | protein | 35 | — | Q8DIN8 |
| m | — | protein | 34 | — | Q8DHA7 |
| x | — | protein | 38 | — | Q9F1R6 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 70 copies · chains A, D, T, I, B, H, L, M, t, C, K, Y, Z, X, a, d, i, b, h, l, m, c, k, y, z, x
- UNL · Unknown ligand · ligand · 52 copies · chains A, C, D, K, T, b, B, H, m, t, X, E, F, I, J, U, Z, a, i, d, h, x, M, c, k, e, j, y, u
- BCR · Beta-carotene · ligand · 20 copies · chains A, I, B, M, t, C, D, F, J, K, Z, T, b, Y, a, i, m, c, k, z, d, f, j, y
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 12 copies · chains A, B, D, L, M, T, C, E, F, X, a, b, d, l, m, t, c, e, f, x
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 10 copies · chains A, C, I, B, D, L, M, K, Y, Z, F, J, a, c, i, b, d, l, m, k, y, z, f, j
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 10 copies · chains A, C, J, D, V, E, B, H, a, c, j, d, v, e, b, h
- PHO · Pheophytin A · ligand · 4 copies · chains A, D, a, d
- PL9 · 2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2, 6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone · ligand · 4 copies · chains A, D, F, X, L, T, a, d, f, x, l, t
- OEX · Ca-MN4-O5 cluster · ligand · 2 copies · chains A, C, a, c
- BCT · Bicarbonate ion · ligand · 2 copies · chains A, D, a, d
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains E, F, e, f
- RRX · (3R)-beta,beta-caroten-3-ol · ligand · 2 copies · chains H, X, h, x
- HEC · Heme C · ligand · 2 copies · chains V, v
- CA · Calcium ion · metal · 7 copies · chains B, O, V, b, c, o, v
- MG · Magnesium ion · metal · 4 copies · chains J, K, j, k, y
- FE2 · Fe (II) ion · metal · 2 copies · chains A, D, a, d
- CL · Chloride ion · ion · 5 copies · chains A, D, C, a, d, c
- DMS · Dimethyl sulfoxide · additive · 95 copies · chains A, b, D, O, E, B, U, M, H, L, a, C, V, I, F, i, o, d, e, u, h, m, c, v, t, f
- HTG · heptyl 1-thio-beta-D-glucopyranoside · additive · 22 copies · chains B, a, o, O, C, D, H, A, b, U, V, c, d, h, v
- LMT · Dodecyl-beta-D-maltoside · additive · 19 copies · chains A, D, O, b, B, H, X, C, I, E, F, J, M, l, m, L, T, Z, a, d, h, c, i, j, t, z
- GOL · Glycerol · additive · 5 copies · chains A, C, V, D, O, b, a, c, v, e
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 5ZZN · Crystal structure of photosystem II from an SQDG-deficient mutant of Thermosynechococcus… · the same entry in another collection · chain K against K, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P0A444
- Every structure of UniProt Q8DIQ1
- Every structure of UniProt Q8DIF8
- Every structure of UniProt Q8CM25
- Every structure of UniProt Q8DIP0
- Every structure of UniProt Q8DIN9
- Every structure of UniProt Q8DJ43
- Every structure of UniProt Q8DJZ6
- Every structure of UniProt P59087
- Every structure of UniProt Q9F1K9
- Every structure of UniProt Q8DIN8
- Every structure of UniProt Q8DHA7
- Every structure of UniProt P0A431
- Every structure of UniProt Q8DIQ0
- Every structure of UniProt Q9F1L5
- Every structure of UniProt P0A386
- Every structure of UniProt Q8DJI1
- Every structure of UniProt Q9F1R6
- Every structure of UniProt Q8DHJ2
- Elsewhere: RCSB PDB 5ZZN · PDBe 5ZZN · UniProt P0A444 · UniProt Q8DIQ1 · UniProt Q8DIF8 · UniProt Q8CM25 · UniProt Q8DIP0 · UniProt Q8DIN9 · UniProt Q8DJ43 · UniProt Q8DJZ6 · UniProt P59087 · UniProt Q9F1K9 · UniProt Q8DIN8 · UniProt Q8DHA7 · UniProt P0A431 · UniProt Q8DIQ0 · UniProt Q9F1L5 · UniProt P0A386 · UniProt Q8DJI1 · UniProt Q9F1R6 · UniProt Q8DHJ2
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